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ORCIDBibTeX records: Matthias Rarey
@article{DBLP:journals/jcamd/HonigFENSLR24,
author = {Sophia M. N. H{\"{o}}nig and
Florian Flachsenberg and
Christiane Ehrt and
Alexander Neumann and
Robert Schmidt and
Christian Lemmen and
Matthias Rarey},
title = {SpaceGrow: efficient shape-based virtual screening of billion-sized
combinatorial fragment spaces},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {13},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00551-7},
doi = {10.1007/S10822-024-00551-7},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HonigFENSLR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FlachsenbergEGR24,
author = {Florian Flachsenberg and
Christiane Ehrt and
Torben Gutermuth and
Matthias Rarey},
title = {Redocking the {PDB}},
journal = {J. Chem. Inf. Model.},
volume = {64},
number = {1},
pages = {219--237},
year = {2024},
url = {https://doi.org/10.1021/acs.jcim.3c01573},
doi = {10.1021/ACS.JCIM.3C01573},
timestamp = {Fri, 26 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FlachsenbergEGR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MeyenburgDBR23,
author = {Christian Meyenburg and
Uschi Dolfus and
Hans Briem and
Matthias Rarey},
title = {Galileo: Three-dimensional searching in large combinatorial fragment
spaces on the example of pharmacophores},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {1},
pages = {1--16},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00485-y},
doi = {10.1007/S10822-022-00485-Y},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MeyenburgDBR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DiedrichKBR23,
author = {Konrad Diedrich and
Bennet Krause and
Ole Berg and
Matthias Rarey},
title = {PoseEdit: enhanced ligand binding mode communication by interactive
2D diagrams},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {10},
pages = {491--503},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00522-4},
doi = {10.1007/S10822-023-00522-4},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DiedrichKBR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/GonzalezPonceAHKMMRTVZ23,
author = {Karla Gonzalez{-}Ponce and
Carolina Horta Andrade and
Fiona Hunter and
Johannes Kirchmair and
Karina Mart{\'{\i}}nez{-}Mayorga and
Jos{\'{e}} L. Medina{-}Franco and
Matthias Rarey and
Alexander Tropsha and
Alexandre Varnek and
Barbara Zdrazil},
title = {School of cheminformatics in Latin America},
journal = {J. Cheminformatics},
volume = {15},
number = {1},
pages = {82},
year = {2023},
url = {https://doi.org/10.1186/s13321-023-00758-0},
doi = {10.1186/S13321-023-00758-0},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/GonzalezPonceAHKMMRTVZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GutermuthSSR23,
author = {Torben Gutermuth and
Jochen Sieg and
Tim Stohn and
Matthias Rarey},
title = {Modeling with Alternate Locations in X-ray Protein Structures},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {8},
pages = {2573--2585},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c00100},
doi = {10.1021/ACS.JCIM.3C00100},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/GutermuthSSR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GraefER23,
author = {Joel Graef and
Christiane Ehrt and
Matthias Rarey},
title = {Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable
Binding Site Detection and Descriptor Calculation with DoGSite3},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {10},
pages = {3128--3137},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c00336},
doi = {10.1021/ACS.JCIM.3C00336},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/GraefER23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DolfusBGR23,
author = {Uschi Dolfus and
Hans Briem and
Torben Gutermuth and
Matthias Rarey},
title = {Full Modification Control over Retrosynthetic Routes for Guided Optimization
of Lead Structures},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {21},
pages = {6587--6597},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c01155},
doi = {10.1021/ACS.JCIM.3C01155},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/DolfusBGR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lwa/PoppingaGDRR23,
author = {Martin Poppinga and
Joel Graef and
Konrad Diedrich and
Matthias Rarey and
Norbert Ritter},
editor = {Michael Leyer and
Johannes Wichmann},
title = {Database and Workflow Optimizations for Spatial-Geometric Queries
in GeoMine},
booktitle = {Lernen, Wissen, Daten, Analysen {(LWDA)} Conference Proceedings, Marburg,
Germany, October 9-11, 2023},
series = {{CEUR} Workshop Proceedings},
volume = {3630},
pages = {86--97},
publisher = {CEUR-WS.org},
year = {2023},
url = {https://ceur-ws.org/Vol-3630/LWDA2023-paper8.pdf},
timestamp = {Wed, 07 Feb 2024 16:02:39 +0100},
biburl = {https://dblp.org/rec/conf/lwa/PoppingaGDRR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PennerMBFGTMR22,
author = {Patrick Penner and
Virginie Y. Martiny and
Louis Bellmann and
Florian Flachsenberg and
Marcus Gastreich and
Isabelle Theret and
Christophe Meyer and
Matthias Rarey},
title = {FastGrow: on-the-fly growing and its application to {DYRK1A}},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {9},
pages = {639--651},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00469-y},
doi = {10.1007/S10822-022-00469-Y},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PennerMBFGTMR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/HarrenMHRG22,
author = {Tobias Harren and
Hans Matter and
Gerhard Hessler and
Matthias Rarey and
Christoph Grebner},
title = {Interpretation of Structure-Activity Relationships in Real-World Drug
Design Data Sets Using Explainable Artificial Intelligence},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {3},
pages = {447--462},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c01263},
doi = {10.1021/ACS.JCIM.1C01263},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/HarrenMHRG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BellmannPGR22,
author = {Louis Bellmann and
Patrick Penner and
Marcus Gastreich and
Matthias Rarey},
title = {Comparison of Combinatorial Fragment Spaces and Its Application to
Ultralarge Make-on-Demand Compound Catalogs},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {3},
pages = {553--566},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c01378},
doi = {10.1021/ACS.JCIM.1C01378},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BellmannPGR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/PennerGSMSR22,
author = {Patrick Penner and
Wolfgang Guba and
Robert Schmidt and
Agnes Meyder and
Martin Stahl and
Matthias Rarey},
title = {The Torsion Library: Semiautomated Improvement of Torsion Rules with
SMARTScompare},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {7},
pages = {1644--1653},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00043},
doi = {10.1021/ACS.JCIM.2C00043},
timestamp = {Thu, 16 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/PennerGSMSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/RareyNW22,
author = {Matthias Rarey and
Marc C. Nicklaus and
Wendy Warr},
title = {Special Issue on Reaction Informatics and Chemical Space},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {9},
pages = {2009--2010},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00390},
doi = {10.1021/ACS.JCIM.2C00390},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/RareyNW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/WarrNNR22,
author = {Wendy A. Warr and
Marc C. Nicklaus and
Christos A. Nicolaou and
Matthias Rarey},
title = {Exploration of Ultralarge Compound Collections for Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {9},
pages = {2021--2034},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00224},
doi = {10.1021/ACS.JCIM.2C00224},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/WarrNNR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchmidtKR22,
author = {Robert Schmidt and
Raphael Klein and
Matthias Rarey},
title = {Maximum Common Substructure Searching in Combinatorial Make-on-Demand
Compound Spaces},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {9},
pages = {2133--2150},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c00640},
doi = {10.1021/ACS.JCIM.1C00640},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SchmidtKR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BellmannKR22,
author = {Louis Bellmann and
Raphael Klein and
Matthias Rarey},
title = {Calculating and Optimizing Physicochemical Property Distributions
of Large Combinatorial Fragment Spaces},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {11},
pages = {2800--2810},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00334},
doi = {10.1021/ACS.JCIM.2C00334},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BellmannKR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DolfusBR22,
author = {Uschi Dolfus and
Hans Briem and
Matthias Rarey},
title = {Synthesis-Aware Generation of Structural Analogues},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {15},
pages = {3565--3576},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00246},
doi = {10.1021/ACS.JCIM.2C00246},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/DolfusBR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DolfusBR22a,
author = {Uschi Dolfus and
Hans Briem and
Matthias Rarey},
title = {Visualizing Generic Reaction Patterns},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {19},
pages = {4680--4689},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00992},
doi = {10.1021/ACS.JCIM.2C00992},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/DolfusBR22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Schoning-Stierand22,
author = {Katrin Sch{\"{o}}ning{-}Stierand and
Konrad Diedrich and
Christiane Ehrt and
Florian Flachsenberg and
Joel Graef and
Jochen Sieg and
Patrick Penner and
Martin Poppinga and
Annett Ungeth{\"{u}}m and
Matthias Rarey},
title = {Proteins\emph{Plus}: a comprehensive collection of web-based molecular
modeling tools},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {611--615},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac305},
doi = {10.1093/NAR/GKAC305},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Schoning-Stierand22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiedrichGSR21,
author = {Konrad Diedrich and
Joel Graef and
Katrin Sch{\"{o}}ning{-}Stierand and
Matthias Rarey},
title = {GeoMine: interactive pattern mining of protein-ligand interfaces in
the Protein Data Bank},
journal = {Bioinform.},
volume = {37},
number = {3},
pages = {424--425},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa693},
doi = {10.1093/BIOINFORMATICS/BTAA693},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiedrichGSR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/FlachsenbergR21,
author = {Florian Flachsenberg and
Matthias Rarey},
title = {LSLOpt: An open-source implementation of the step-length controlled
{LSL-BFGS} algorithm},
journal = {J. Comput. Chem.},
volume = {42},
number = {15},
pages = {1095--1100},
year = {2021},
url = {https://doi.org/10.1002/jcc.26522},
doi = {10.1002/JCC.26522},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/FlachsenbergR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchmidtKHR21,
author = {Robert Schmidt and
Florian Krull and
Anna Lina Heinzke and
Matthias Rarey},
title = {Disconnected Maximum Common Substructures under Constraints},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {1},
pages = {167--178},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.0c00741},
doi = {10.1021/ACS.JCIM.0C00741},
timestamp = {Thu, 16 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SchmidtKHR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BellmannPR21,
author = {Louis Bellmann and
Patrick Penner and
Matthias Rarey},
title = {Topological Similarity Search in Large Combinatorial Fragment Spaces},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {1},
pages = {238--251},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.0c00850},
doi = {10.1021/ACS.JCIM.0C00850},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BellmannPR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/RareyNW21,
author = {Matthias Rarey and
Marc C. Nicklaus and
Wendy A. Warr},
title = {Call for Papers for the Special Issue: From Reaction Informatics to
Chemical Space},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {4},
pages = {1531--1532},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.1c00321},
doi = {10.1021/ACS.JCIM.1C00321},
timestamp = {Fri, 03 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/RareyNW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MerzACRSTWW20,
author = {Kenneth M. Merz Jr. and
Rommie E. Amaro and
Zoe Cournia and
Matthias Rarey and
Thereza A. Soares and
Alexander Tropsha and
Habibah A. Wahab and
Renxiao Wang},
title = {Editorial: Method and Data Sharing and Reproducibility of Scientific
Results},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {12},
pages = {5868--5869},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c01389},
doi = {10.1021/ACS.JCIM.0C01389},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MerzACRSTWW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/PennerMGGDBR20,
author = {Patrick Penner and
Virginie Y. Martiny and
Arnaud Gohier and
Marcus Gastreich and
Pierre Ducrot and
David Brown and
Matthias Rarey},
title = {Shape-Based Descriptors for Efficient Structure-Based Fragment Growing},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {12},
pages = {6269--6281},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00920},
doi = {10.1021/ACS.JCIM.0C00920},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/PennerMGGDBR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FlachsenbergMSP20,
author = {Florian Flachsenberg and
Agnes Meyder and
Kai Sommer and
Patrick Penner and
Matthias Rarey},
title = {A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand
Poses},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {12},
pages = {6502--6522},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c01095},
doi = {10.1021/ACS.JCIM.0C01095},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/FlachsenbergMSP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Schoning-Stierand20,
author = {Katrin Sch{\"{o}}ning{-}Stierand and
Konrad Diedrich and
Rainer F{\"{a}}hrrolfes and
Florian Flachsenberg and
Agnes Meyder and
Eva Nittinger and
Ruben Steinegger and
Matthias Rarey},
title = {Proteins\emph{Plus}: interactive analysis of protein-ligand binding
interfaces},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Webserver-Issue},
pages = {W48--W53},
year = {2020},
url = {https://doi.org/10.1093/nar/gkaa235},
doi = {10.1093/NAR/GKAA235},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Schoning-Stierand20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MeyderKSFFFR19,
author = {Agnes Meyder and
Stefanie Kampen and
Jochen Sieg and
Rainer F{\"{a}}hrrolfes and
Nils{-}Ole Friedrich and
Florian Flachsenberg and
Matthias Rarey},
title = {StructureProfiler: an all-in-one tool for 3D protein structure profiling},
journal = {Bioinform.},
volume = {35},
number = {5},
pages = {874--876},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty692},
doi = {10.1093/BIOINFORMATICS/BTY692},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MeyderKSFFFR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FriedrichFMSKR19,
author = {Nils{-}Ole Friedrich and
Florian Flachsenberg and
Agnes Meyder and
Kai Sommer and
Johannes Kirchmair and
Matthias Rarey},
title = {Conformator: {A} Novel Method for the Generation of Conformer Ensembles},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {2},
pages = {731--742},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00704},
doi = {10.1021/ACS.JCIM.8B00704},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/FriedrichFMSKR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KlambauerHR19,
author = {G{\"{u}}nter Klambauer and
Sepp Hochreiter and
Matthias Rarey},
title = {Machine Learning in Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {3},
pages = {945--946},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00136},
doi = {10.1021/ACS.JCIM.9B00136},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/KlambauerHR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SiegFR19,
author = {Jochen Sieg and
Florian Flachsenberg and
Matthias Rarey},
title = {In Need of Bias Control: Evaluating Chemical Data for Machine Learning
in Structure-Based Virtual Screening},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {3},
pages = {947--961},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00712},
doi = {10.1021/ACS.JCIM.8B00712},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SiegFR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchmidtEOEMR19,
author = {Robert Schmidt and
Emanuel S. R. Ehmki and
Farina Ohm and
Hans{-}Christian Ehrlich and
Andriy Mashychev and
Matthias Rarey},
title = {Comparing Molecular Patterns Using the Example of {SMARTS:} Theory
and Algorithms},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {6},
pages = {2560--2571},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00250},
doi = {10.1021/ACS.JCIM.9B00250},
timestamp = {Thu, 16 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SchmidtEOEMR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/EhmkiSOR19,
author = {Emanuel S. R. Ehmki and
Robert Schmidt and
Farina Ohm and
Matthias Rarey},
title = {Comparing Molecular Patterns Using the Example of {SMARTS:} Applications
and Filter Collection Analysis},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {6},
pages = {2572--2586},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00249},
doi = {10.1021/ACS.JCIM.9B00249},
timestamp = {Thu, 16 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/EhmkiSOR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BellmannPR19,
author = {Louis Bellmann and
Patrick Penner and
Matthias Rarey},
title = {Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive
Subgraph Enumeration},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {11},
pages = {4625--4635},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00571},
doi = {10.1021/ACS.JCIM.9B00571},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BellmannPR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/NittingerFBLKR18,
author = {Eva Nittinger and
Florian Flachsenberg and
Stefan Bietz and
Gudrun Lange and
Robert Klein and
Matthias Rarey},
title = {Placement of Water Molecules in Protein Structures: From Large-Scale
Evaluations to Single-Case Examples},
journal = {J. Chem. Inf. Model.},
volume = {58},
number = {8},
pages = {1625--1637},
year = {2018},
url = {https://doi.org/10.1021/acs.jcim.8b00271},
doi = {10.1021/ACS.JCIM.8B00271},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/NittingerFBLKR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/HochreiterKR18,
author = {Sepp Hochreiter and
G{\"{u}}nter Klambauer and
Matthias Rarey},
title = {Machine Learning in Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {58},
number = {9},
pages = {1723--1724},
year = {2018},
url = {https://doi.org/10.1021/acs.jcim.8b00478},
doi = {10.1021/ACS.JCIM.8B00478},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/HochreiterKR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BehrenR17,
author = {Mathias M. von Behren and
Matthias Rarey},
title = {Ligand-based virtual screening under partial shape constraints},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {335--347},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0011-z},
doi = {10.1007/S10822-017-0011-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BehrenR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FlachsenbergAR17,
author = {Florian Flachsenberg and
Niek Andresen and
Matthias Rarey},
title = {RingDecomposerLib: An Open-Source Implementation of Unique Ring Families
and Other Cycle Bases},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {2},
pages = {122--126},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.6b00736},
doi = {10.1021/ACS.JCIM.6B00736},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FlachsenbergAR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/InhesterBHSR17,
author = {Therese Inhester and
Stefan Bietz and
Matthias Hilbig and
Robert Schmidt and
Matthias Rarey},
title = {Index-Based Searching of Interaction Patterns in Large Collections
of Protein-Ligand Interfaces},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {2},
pages = {148--158},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.6b00561},
doi = {10.1021/ACS.JCIM.6B00561},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/InhesterBHSR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FriedrichMKSFRK17,
author = {Nils{-}Ole Friedrich and
Agnes Meyder and
Christina de Bruyn Kops and
Kai Sommer and
Florian Flachsenberg and
Matthias Rarey and
Johannes Kirchmair},
title = {High-Quality Dataset of Protein-Bound Ligand Conformations and Its
Application to Benchmarking Conformer Ensemble Generators},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {3},
pages = {529--539},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.6b00613},
doi = {10.1021/ACS.JCIM.6B00613},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FriedrichMKSFRK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/InhesterNSSBR17,
author = {Therese Inhester and
Eva Nittinger and
Kai Sommer and
Pascal Schmidt and
Stefan Bietz and
Matthias Rarey},
title = {\emph{NAOMI}nova: Interactive Geometric Analysis of Noncovalent Interactions
in Macromolecular Structures},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {9},
pages = {2132--2142},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00291},
doi = {10.1021/ACS.JCIM.7B00291},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/InhesterNSSBR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MeyderNLKR17,
author = {Agnes Meyder and
Eva Nittinger and
Gudrun Lange and
Robert Klein and
Matthias Rarey},
title = {Estimating Electron Density Support for Individual Atoms and Molecular
Fragments in X-ray Structures},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {10},
pages = {2437--2447},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00391},
doi = {10.1021/ACS.JCIM.7B00391},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MeyderNLKR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FriedrichKFSRK17,
author = {Nils{-}Ole Friedrich and
Christina de Bruyn Kops and
Florian Flachsenberg and
Kai Sommer and
Matthias Rarey and
Johannes Kirchmair},
title = {Benchmarking Commercial Conformer Ensemble Generators},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {11},
pages = {2719--2728},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00505},
doi = {10.1021/ACS.JCIM.7B00505},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/FriedrichKFSRK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FahrrolfesBFMNO17,
author = {Rainer F{\"{a}}hrrolfes and
Stefan Bietz and
Florian Flachsenberg and
Agnes Meyder and
Eva Nittinger and
Thomas Otto and
Andrea Volkamer and
Matthias Rarey},
title = {ProteinsPlus: a web portal for structure analysis of macromolecules},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Webserver-Issue},
pages = {W337--W343},
year = {2017},
url = {https://doi.org/10.1093/nar/gkx333},
doi = {10.1093/NAR/GKX333},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FahrrolfesBFMNO17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BehrenBNR16,
author = {Mathias M. von Behren and
Stefan Bietz and
Eva Nittinger and
Matthias Rarey},
title = {mRAISE: an alternative algorithmic approach to ligand-based virtual
screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {583--594},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9940-1},
doi = {10.1007/S10822-016-9940-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BehrenBNR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GubaMRH16,
author = {Wolfgang Guba and
Agnes Meyder and
Matthias Rarey and
J{\'{e}}r{\^{o}}me Hert},
title = {Torsion Library Reloaded: {A} New Version of Expert-Derived {SMARTS}
Rules for Assessing Conformations of Small Molecules},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {1},
pages = {1--5},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.5b00522},
doi = {10.1021/ACS.JCIM.5B00522},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/GubaMRH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LangFLR16,
author = {Tobias Lang and
Florian Flachsenberg and
Ulrike von Luxburg and
Matthias Rarey},
title = {Feasibility of Active Machine Learning for Multiclass Compound Classification},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {1},
pages = {12--20},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.5b00332},
doi = {10.1021/ACS.JCIM.5B00332},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LangFLR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BietzR16,
author = {Stefan Bietz and
Matthias Rarey},
title = {{SIENA:} Efficient Compilation of Selective Protein Binding Site Ensembles},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {1},
pages = {248--259},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.5b00588},
doi = {10.1021/ACS.JCIM.5B00588},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/BietzR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SommerFBHIR16,
author = {Kai Sommer and
Nils{-}Ole Friedrich and
Stefan Bietz and
Matthias Hilbig and
Therese Inhester and
Matthias Rarey},
title = {{UNICON:} {A} Powerful and Easy-to-Use Compound Library Converter},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {6},
pages = {1105--1111},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.6b00069},
doi = {10.1021/ACS.JCIM.6B00069},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SommerFBHIR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LauckR16,
author = {Florian Lauck and
Matthias Rarey},
title = {FSees: Customized Enumeration of Chemical Subspaces with Limited Main
Memory Consumption},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {9},
pages = {1641--1653},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.6b00117},
doi = {10.1021/ACS.JCIM.6B00117},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LauckR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MerzRTW15,
author = {Kenneth M. Merz Jr. and
Matthias Rarey and
Alexander Tropsha and
Habibah A. Wahab},
title = {Letter from the Editors},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {4},
pages = {719--720},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00180},
doi = {10.1021/ACS.JCIM.5B00180},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MerzRTW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/NittingerSLR15,
author = {Eva Nittinger and
Nadine Schneider and
Gudrun Lange and
Matthias Rarey},
title = {Evidence of Water Molecules - {A} Statistical Evaluation of Water
Molecules Based on Electron Density},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {4},
pages = {771--783},
year = {2015},
url = {https://doi.org/10.1021/ci500662d},
doi = {10.1021/CI500662D},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/NittingerSLR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/WagenerOFR15,
author = {Markus Wagener and
Frank Oellien and
Uli Fechner and
Matthias Rarey},
title = {10th {ICCS/GCC} Conference: 40 Years of Cheminformatics},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {6},
pages = {1087},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00361},
doi = {10.1021/ACS.JCIM.5B00361},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/WagenerOFR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BietzSHR15,
author = {Stefan Bietz and
Karen T. Schomburg and
Matthias Hilbig and
Matthias Rarey},
title = {Discriminative Chemical Patterns: Automatic and Interactive Design},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {8},
pages = {1535--1546},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00323},
doi = {10.1021/ACS.JCIM.5B00323},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BietzSHR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BietzR15,
author = {Stefan Bietz and
Matthias Rarey},
title = {{ASCONA:} Rapid Detection and Alignment of Protein Binding Site Conformations},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {8},
pages = {1747--1756},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00210},
doi = {10.1021/ACS.JCIM.5B00210},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/BietzR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/HilbigR15,
author = {Matthias Hilbig and
Matthias Rarey},
title = {{MONA} 2: {A} Light Cheminformatics Platform for Interactive Compound
Library Processing},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {10},
pages = {2071--2078},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00292},
doi = {10.1021/ACS.JCIM.5B00292},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/HilbigR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HenzlerUHR14,
author = {Angela M. Henzler and
Sascha Urbaczek and
Matthias Hilbig and
Matthias Rarey},
title = {An integrated approach to knowledge-driven structure-based virtual
screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {927--939},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9769-4},
doi = {10.1007/S10822-014-9769-4},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HenzlerUHR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/BietzUSR14,
author = {Stefan Bietz and
Sascha Urbaczek and
Benjamin Schulz and
Matthias Rarey},
title = {Protoss: a holistic approach to predict tautomers and protonation
states in protein-ligand complexes},
journal = {J. Cheminformatics},
volume = {6},
number = {1},
pages = {12},
year = {2014},
url = {https://doi.org/10.1186/1758-2946-6-12},
doi = {10.1186/1758-2946-6-12},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/BietzUSR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/SchomburgR14,
author = {Karen T. Schomburg and
Matthias Rarey},
title = {Facing the challenges of computational target prediction},
journal = {J. Cheminformatics},
volume = {6},
number = {{S-1}},
pages = {3},
year = {2014},
url = {https://doi.org/10.1186/1758-2946-6-S1-O3},
doi = {10.1186/1758-2946-6-S1-O3},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/SchomburgR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/VennmannSLR14,
author = {Eva Vennmann and
Nadine Schneider and
Gudrun Lange and
Matthias Rarey},
title = {Elucidating protein-protein interactions using the {HYDE} scoring
function},
journal = {J. Cheminformatics},
volume = {6},
number = {{S-1}},
pages = {36},
year = {2014},
url = {https://doi.org/10.1186/1758-2946-6-S1-P36},
doi = {10.1186/1758-2946-6-S1-P36},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/VennmannSLR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/StierandHWLR14,
author = {Katrin Stierand and
Tim Harder and
Lothar Wissler and
Christian Lemmen and
Matthias Rarey},
title = {Accessing Open {PHACTS:} interactive exploration of compounds and
targets from the semantic web},
journal = {J. Cheminformatics},
volume = {6},
number = {{S-1}},
pages = {52},
year = {2014},
url = {https://doi.org/10.1186/1758-2946-6-S1-P52},
doi = {10.1186/1758-2946-6-S1-P52},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/StierandHWLR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/UrbaczekKR14,
author = {Sascha Urbaczek and
Adrian Kolodzik and
Matthias Rarey},
title = {The Valence State Combination Model: {A} Generic Framework for Handling
Tautomers and Protonation States},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {3},
pages = {756--766},
year = {2014},
url = {https://doi.org/10.1021/ci400724v},
doi = {10.1021/CI400724V},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/UrbaczekKR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchomburgBBHUR14,
author = {Karen Schomburg and
Stefan Bietz and
Hans Briem and
Angela M. Henzler and
Sascha Urbaczek and
Matthias Rarey},
title = {Facing the Challenges of Structure-Based Target Prediction by Inverse
Virtual Screening},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {6},
pages = {1676--1686},
year = {2014},
url = {https://doi.org/10.1021/ci500130e},
doi = {10.1021/CI500130E},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SchomburgBBHUR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchomburgR14,
author = {Karen Schomburg and
Matthias Rarey},
title = {Benchmark Data Sets for Structure-Based Computational Target Prediction},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {8},
pages = {2261--2274},
year = {2014},
url = {https://doi.org/10.1021/ci500131x},
doi = {10.1021/CI500131X},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SchomburgR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchneiderLHKR13,
author = {Nadine Schneider and
Gudrun Lange and
Sally A. Hindle and
Robert Klein and
Matthias Rarey},
title = {A consistent description of HYdrogen bond and DEhydration energies
in protein-ligand complexes: methods behind the {HYDE} scoring function},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {15--29},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9626-2},
doi = {10.1007/S10822-012-9626-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SchneiderLHKR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WirthVZRMRS13,
author = {Matthias Wirth and
Andrea Volkamer and
Vincent Zoete and
Friedrich Rippmann and
Olivier Michielin and
Matthias Rarey and
Wolfgang H. B. Sauer},
title = {Protein pocket and ligand shape comparison and its application in
virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {511--524},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9659-1},
doi = {10.1007/S10822-013-9659-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WirthVZRMRS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/ScharferSR13,
author = {Christin Sch{\"{a}}rfer and
Tanja Schulz{-}Gasch and
Matthias Rarey},
title = {TorsionAnalyzer: exploring conformational space},
journal = {J. Cheminformatics},
volume = {5},
number = {{S-1}},
pages = {3},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-S1-P3},
doi = {10.1186/1758-2946-5-S1-P3},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/ScharferSR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/RareyKU13,
author = {Matthias Rarey and
Adrian Kolodzik and
Sascha Urbaczek},
title = {Let's talk about rings},
journal = {J. Cheminformatics},
volume = {5},
number = {{S-1}},
pages = {8},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-S1-O8},
doi = {10.1186/1758-2946-5-S1-O8},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/RareyKU13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/HeinzerlingR13,
author = {Lennart Heinzerling and
Matthias Rarey},
title = {Force-field-based minimizations of protein-ligand complexes in the
blink of an eye},
journal = {J. Cheminformatics},
volume = {5},
number = {{S-1}},
pages = {14},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-S1-P14},
doi = {10.1186/1758-2946-5-S1-P14},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/HeinzerlingR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/HilbigUGHR13,
author = {Matthias Hilbig and
Sascha Urbaczek and
Inken Groth and
Stefan Heuser and
Matthias Rarey},
title = {{MONA} - Interactive manipulation of molecule collections},
journal = {J. Cheminformatics},
volume = {5},
pages = {38},
year = {2013},
url = {http://www.jcheminf.com/content/5/1/38},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/HilbigUGHR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/UrbaczekKGHR13,
author = {Sascha Urbaczek and
Adrian Kolodzik and
Inken Groth and
Stefan Heuser and
Matthias Rarey},
title = {Reading {PDB:} Perception of Molecules from 3D Atomic Coordinates},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {1},
pages = {76--87},
year = {2013},
url = {https://doi.org/10.1021/ci300358c},
doi = {10.1021/CI300358C},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/UrbaczekKGHR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BehrenVHSUR13,
author = {Mathias M. von Behren and
Andrea Volkamer and
Angela M. Henzler and
Karen Schomburg and
Sascha Urbaczek and
Matthias Rarey},
title = {Fast Protein Binding Site Comparison via an Index-Based Screening
Technology},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {2},
pages = {411--422},
year = {2013},
url = {https://doi.org/10.1021/ci300469h},
doi = {10.1021/CI300469H},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/BehrenVHSUR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/EhrlichHR13,
author = {Hans{-}Christian Ehrlich and
Angela M. Henzler and
Matthias Rarey},
title = {Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated
Fragment Spaces},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {7},
pages = {1676--1688},
year = {2013},
url = {https://doi.org/10.1021/ci400107k},
doi = {10.1021/CI400107K},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/EhrlichHR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VolkamerKRR12,
author = {Andrea Volkamer and
Daniel Kuhn and
Friedrich Rippmann and
Matthias Rarey},
title = {DoGSiteScorer: a web server for automatic binding site prediction,
analysis and druggability assessment},
journal = {Bioinform.},
volume = {28},
number = {15},
pages = {2074--2075},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts310},
doi = {10.1093/BIOINFORMATICS/BTS310},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VolkamerKRR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Rarey12,
author = {Matthias Rarey},
title = {Some thoughts on the "A" in computer-aided molecular design},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {113--114},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9507-0},
doi = {10.1007/S10822-011-9507-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Rarey12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchneiderHLKABBCGLR12,
author = {Nadine Schneider and
Sally A. Hindle and
Gudrun Lange and
Robert Klein and
J{\"{u}}rgen Albrecht and
Hans Briem and
Kristin Beyer and
Holger Clau{\ss}en and
Marcus Gastreich and
Christian Lemmen and
Matthias Rarey},
title = {Substantial improvements in large-scale redocking and screening using
the novel {HYDE} scoring function},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {6},
pages = {701--723},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9531-0},
doi = {10.1007/S10822-011-9531-0},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SchneiderHLKABBCGLR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/HeinzerlingKR12,
author = {Lennart Heinzerling and
Robert Klein and
Matthias Rarey},
title = {Fast force field-based optimization of protein-ligand complexes with
graphics processor},
journal = {J. Comput. Chem.},
volume = {33},
number = {32},
pages = {2554--2565},
year = {2012},
url = {https://doi.org/10.1002/jcc.23094},
doi = {10.1002/JCC.23094},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/HeinzerlingKR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/HilbigR12,
author = {Matthias Hilbig and
Matthias Rarey},
title = {Aligning chemical structure diagrams with local search},
journal = {J. Cheminformatics},
volume = {4},
number = {{S-1}},
pages = {4},
year = {2012},
url = {https://doi.org/10.1186/1758-2946-4-S1-O4},
doi = {10.1186/1758-2946-4-S1-O4},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/HilbigR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/EhrlichR12,
author = {Hans{-}Christian Ehrlich and
Matthias Rarey},
title = {Systematic benchmark of substructure search in molecular graphs -
From Ullmann to {VF2}},
journal = {J. Cheminformatics},
volume = {4},
pages = {13},
year = {2012},
url = {https://doi.org/10.1186/1758-2946-4-13},
doi = {10.1186/1758-2946-4-13},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/EhrlichR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/HenzlerUSR12,
author = {Angela M. Henzler and
Sascha Urbaczek and
Benjamin Schulz and
Matthias Rarey},
title = {A flexible-hydrogen interaction model for protein-ligand docking},
journal = {J. Cheminformatics},
volume = {4},
number = {{S-1}},
pages = {14},
year = {2012},
url = {https://doi.org/10.1186/1758-2946-4-S1-P14},
doi = {10.1186/1758-2946-4-S1-P14},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/HenzlerUSR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/ScharferSR12,
author = {Christin Sch{\"{a}}rfer and
Tanja Schulz{-}Gasch and
Matthias Rarey},
title = {Systematic search for pairwise dependencies of torsion angles},
journal = {J. Cheminformatics},
volume = {4},
number = {{S-1}},
pages = {36},
year = {2012},
url = {https://doi.org/10.1186/1758-2946-4-S1-P36},
doi = {10.1186/1758-2946-4-S1-P36},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/ScharferSR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/VolkamerKGRR12,
author = {Andrea Volkamer and
Daniel Kuhn and
Thomas Grombacher and
Friedrich Rippmann and
Matthias Rarey},
title = {Combining Global and Local Measures for Structure-Based Druggability
Predictions},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {2},
pages = {360--372},
year = {2012},
url = {https://doi.org/10.1021/ci200454v},
doi = {10.1021/CI200454V},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/VolkamerKGRR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LesselWFR12,
author = {Uta F. Lessel and
Bernd Wellenzohn and
J. Robert Fischer and
Matthias Rarey},
title = {Design of Combinatorial Libraries for the Exploration of Virtual Hits
from Fragment Space Searches with LoFT},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {2},
pages = {373--379},
year = {2012},
url = {https://doi.org/10.1021/ci2003957},
doi = {10.1021/CI2003957},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LesselWFR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Schulz-GaschSGR12,
author = {Tanja Schulz{-}Gasch and
Christin Sch{\"{a}}rfer and
Wolfgang Guba and
Matthias Rarey},
title = {{TFD:} Torsion Fingerprints As a New Measure To Compare Small Molecule
Conformations},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {6},
pages = {1499--1512},
year = {2012},
url = {https://doi.org/10.1021/ci2002318},
doi = {10.1021/CI2002318},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/Schulz-GaschSGR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KolodzikUR12,
author = {Adrian Kolodzik and
Sascha Urbaczek and
Matthias Rarey},
title = {Unique Ring Families: {A} Chemically Meaningful Description of Molecular
Ring Topologies},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {8},
pages = {2013--2021},
year = {2012},
url = {https://doi.org/10.1021/ci200629w},
doi = {10.1021/CI200629W},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/KolodzikUR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/EhrlichVR12,
author = {Hans{-}Christian Ehrlich and
Andrea Volkamer and
Matthias Rarey},
title = {Searching for Substructures in Fragment Spaces},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {12},
pages = {3181--3189},
year = {2012},
url = {https://doi.org/10.1021/ci300283a},
doi = {10.1021/CI300283A},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/EhrlichVR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LippertSRGR11,
author = {Tobias Lippert and
Tanja Schulz{-}Gasch and
Olivier Roche and
Wolfgang Guba and
Matthias Rarey},
title = {De novo design by pharmacophore-based searches in fragment spaces},
journal = {J. Comput. Aided Mol. Des.},
volume = {25},
number = {10},
pages = {931--945},
year = {2011},
url = {https://doi.org/10.1007/s10822-011-9473-6},
doi = {10.1007/S10822-011-9473-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LippertSRGR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/EhrlichR11,
author = {Hans{-}Christian Ehrlich and
Matthias Rarey},
title = {Searching substructures in fragment spaces},
journal = {J. Cheminformatics},
volume = {3},
number = {{S-1}},
pages = {11},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-S1-P11},
doi = {10.1186/1758-2946-3-S1-P11},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/EhrlichR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/SchomburgESR11,
author = {Karen Schomburg and
Hans{-}Christian Ehrlich and
Katrin Stierand and
Matthias Rarey},
title = {Chemical pattern visualization in 2D - the SMARTSviewer},
journal = {J. Cheminformatics},
volume = {3},
number = {{S-1}},
pages = {12},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-S1-O12},
doi = {10.1186/1758-2946-3-S1-O12},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/SchomburgESR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/BietzUR11,
author = {Stefan Bietz and
Sascha Urbaczek and
Matthias Rarey},
title = {Hydrogen placement in protein-ligand complexes under consideration
of tautomerism},
journal = {J. Cheminformatics},
volume = {3},
number = {{S-1}},
pages = {13},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-S1-P13},
doi = {10.1186/1758-2946-3-S1-P13},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/BietzUR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/StierandR11,
author = {Katrin Stierand and
Matthias Rarey},
title = {Consistent two-dimensional visualization of protein-ligand complex
series},
journal = {J. Cheminformatics},
volume = {3},
pages = {21},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-21},
doi = {10.1186/1758-2946-3-21},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/StierandR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/SchneiderLKLR11,
author = {Nadine Schneider and
Gudrun Lange and
Robert Klein and
Christian Lemmen and
Matthias Rarey},
title = {HYDEing the false positives - scoring for lead optimization},
journal = {J. Cheminformatics},
volume = {3},
number = {{S-1}},
pages = {29},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-S1-P29},
doi = {10.1186/1758-2946-3-S1-P29},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/SchneiderLKLR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FischerLR11,
author = {J. Robert Fischer and
Uta F. Lessel and
Matthias Rarey},
title = {Improving Similarity-Driven Library Design: Customized Matching and
Regioselective Feature Trees},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {9},
pages = {2156--2163},
year = {2011},
url = {https://doi.org/10.1021/ci200014g},
doi = {10.1021/CI200014G},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FischerLR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/UrbaczekKFLHGSR11,
author = {Sascha Urbaczek and
Adrian Kolodzik and
J. Robert Fischer and
Tobias Lippert and
Stefan Heuser and
Inken Groth and
Tanja Schulz{-}Gasch and
Matthias Rarey},
title = {{NAOMI:} On the Almost Trivial Task of Reading Molecules from Different
File formats},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {12},
pages = {3199--3207},
year = {2011},
url = {https://doi.org/10.1021/ci200324e},
doi = {10.1021/CI200324E},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/UrbaczekKFLHGSR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/VolkamerGR10,
author = {Andrea Volkamer and
Thomas Grombacher and
Matthias Rarey},
title = {Where are the boundaries? Automated pocket detection for druggability
studies},
journal = {J. Cheminformatics},
volume = {2},
number = {{S-1}},
pages = {11},
year = {2010},
url = {https://doi.org/10.1186/1758-2946-2-S1-P11},
doi = {10.1186/1758-2946-2-S1-P11},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/VolkamerGR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/StierandR10,
author = {Katrin Stierand and
Matthias Rarey},
title = {PoseView - molecular interaction patterns at a glance},
journal = {J. Cheminformatics},
volume = {2},
number = {{S-1}},
pages = {50},
year = {2010},
url = {https://doi.org/10.1186/1758-2946-2-S1-P50},
doi = {10.1186/1758-2946-2-S1-P50},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/StierandR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FischerLR10,
author = {J. Robert Fischer and
Uta F. Lessel and
Matthias Rarey},
title = {LoFT: Similarity-Driven Multiobjective Focused Library Design},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {1},
pages = {1--21},
year = {2010},
url = {https://doi.org/10.1021/ci900287p},
doi = {10.1021/CI900287P},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FischerLR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchomburgESR10,
author = {Karen Schomburg and
Hans{-}Christian Ehrlich and
Katrin Stierand and
Matthias Rarey},
title = {From Structure Diagrams to Visual Chemical Patterns},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {9},
pages = {1529--1535},
year = {2010},
url = {https://doi.org/10.1021/ci100209a},
doi = {10.1021/CI100209A},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SchomburgESR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/VolkamerGGR10,
author = {Andrea Volkamer and
Axel Griewel and
Thomas Grombacher and
Matthias Rarey},
title = {Analyzing the Topology of Active Sites: On the Prediction of Pockets
and Subpockets},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {11},
pages = {2041--2052},
year = {2010},
url = {https://doi.org/10.1021/ci100241y},
doi = {10.1021/CI100241Y},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/VolkamerGGR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZalianiBSHSGCLDPR09,
author = {Andrea Zaliani and
Krisztina Boda and
Thomas Seidel and
Achim Herwig and
Christof H. Schwab and
Johann Gasteiger and
Holger Claussen and
Christian Lemmen and
J{\"{o}}rg Degen and
Juri P{\"{a}}rn and
Matthias Rarey},
title = {Second-generation de novo design: a view from a medicinal chemist
perspective},
journal = {J. Comput. Aided Mol. Des.},
volume = {23},
number = {8},
pages = {593--602},
year = {2009},
url = {https://doi.org/10.1007/s10822-009-9291-2},
doi = {10.1007/S10822-009-9291-2},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ZalianiBSHSGCLDPR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LippertR09,
author = {Tobias Lippert and
Matthias Rarey},
title = {Fast automated placement of polar hydrogen atoms in protein-ligand
complexes},
journal = {J. Cheminformatics},
volume = {1},
pages = {13},
year = {2009},
url = {https://doi.org/10.1186/1758-2946-1-13},
doi = {10.1186/1758-2946-1-13},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/LippertR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchlosserR09,
author = {Jochen Schlosser and
Matthias Rarey},
title = {Beyond the Virtual Screening Paradigm: Structure-Based Searching for
New Lead Compounds},
journal = {J. Chem. Inf. Model.},
volume = {49},
number = {4},
pages = {800--809},
year = {2009},
url = {https://doi.org/10.1021/ci9000212},
doi = {10.1021/CI9000212},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SchlosserR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GriewelKSR09,
author = {Axel Griewel and
Ole Kayser and
Jochen Schlosser and
Matthias Rarey},
title = {Conformational Sampling for Large-Scale Virtual Screening: Accuracy
versus Ensemble Size},
journal = {J. Chem. Inf. Model.},
volume = {49},
number = {10},
pages = {2303--2311},
year = {2009},
url = {https://doi.org/10.1021/ci9002415},
doi = {10.1021/CI9002415},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/GriewelKSR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchellhammerR07,
author = {Ingo Schellhammer and
Matthias Rarey},
title = {TrixX: structure-based molecule indexing for large-scale virtual screening
in sublinear time},
journal = {J. Comput. Aided Mol. Des.},
volume = {21},
number = {5},
pages = {223--238},
year = {2007},
url = {https://doi.org/10.1007/s10822-007-9103-5},
doi = {10.1007/S10822-007-9103-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SchellhammerR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParnDR07,
author = {Juri P{\"{a}}rn and
J{\"{o}}rg Degen and
Matthias Rarey},
title = {Exploring fragment spaces under multiple physicochemical constraints},
journal = {J. Comput. Aided Mol. Des.},
volume = {21},
number = {6},
pages = {327--340},
year = {2007},
url = {https://doi.org/10.1007/s10822-007-9121-3},
doi = {10.1007/S10822-007-9121-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParnDR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MaassSSR07,
author = {Patrick C. Maa{\ss} and
Tanja Schulz{-}Gasch and
Martin Stahl and
Matthias Rarey},
title = {Recore: {A} Fast and Versatile Method for Scaffold Hopping Based on
Small Molecule Crystal Structure Conformations},
journal = {J. Chem. Inf. Model.},
volume = {47},
number = {2},
pages = {390--399},
year = {2007},
url = {https://doi.org/10.1021/ci060094h},
doi = {10.1021/CI060094H},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/MaassSSR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FischerR07,
author = {J. Robert Fischer and
Matthias Rarey},
title = {SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual
Screening and Clustering},
journal = {J. Chem. Inf. Model.},
volume = {47},
number = {4},
pages = {1341--1353},
year = {2007},
url = {https://doi.org/10.1021/ci700007b},
doi = {10.1021/CI700007B},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FischerR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StierandMR06,
author = {Katrin Stierand and
Patrick C. Maa{\ss} and
Matthias Rarey},
title = {Molecular complexes at a glance: automated generation of two-dimensional
complex diagrams},
journal = {Bioinform.},
volume = {22},
number = {14},
pages = {1710--1716},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl150},
doi = {10.1093/BIOINFORMATICS/BTL150},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StierandMR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KamperARML06,
author = {Andreas K{\"{a}}mper and
Joannis Apostolakis and
Matthias Rarey and
Christel M. Marian and
Thomas Lengauer},
title = {Fully Automated Flexible Docking of Ligands into Flexible Synthetic
Receptors Using Forward and Inverse Docking Strategies},
journal = {J. Chem. Inf. Model.},
volume = {46},
number = {2},
pages = {903--911},
year = {2006},
url = {https://doi.org/10.1021/ci050467z},
doi = {10.1021/CI050467Z},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/KamperARML06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/GriewelR05,
author = {Axel Griewel and
Matthias Rarey},
editor = {Andrew E. Torda and
Stefan Kurtz and
Matthias Rarey},
title = {From greedy to branch {\&} bound and back: Assessing optimization
strategies for incremental construction molecular docking tools},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2005),
Hamburg, Germany, October 5-7, 2005},
series = {{LNI}},
volume = {{P-71}},
pages = {119--130},
publisher = {{GI}},
year = {2005},
url = {https://dl.gi.de/handle/20.500.12116/24925},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/GriewelR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/gcb/2005,
editor = {Andrew E. Torda and
Stefan Kurtz and
Matthias Rarey},
title = {Proceedings of the German Conference on Bioinformatics {(GCB} 2005),
Hamburg, Germany, October 5-7, 2005},
series = {{LNI}},
volume = {{P-71}},
publisher = {{GI}},
year = {2005},
url = {https://dl.gi.de/handle/20.500.12116/24920},
isbn = {3-88579-400-4},
timestamp = {Tue, 12 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gcb/2005.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CrassAB04,
author = {Torsten Crass and
Iris Antes and
Rico Basekow and
Peer Bork and
Christian Buning and
Maik Christensen and
Holger Claussen and
Christian Ebeling and
Peter Ernst and
Val{\'{e}}rie Gailus{-}Durner and
Karl{-}Heinz Glatting and
Rolf Gohla and
Frank G{\"{o}}{\ss}ling and
Korbinian Grote and
Karsten R. Heidtke and
Alexander Herrmann and
Sean O'Keeffe and
O. Kie{\ss}lich and
Sven Kolibal and
Jan O. Korbel and
Thomas Lengauer and
Ines Liebich and
Mark van der Linden and
Hannes Luz and
Kathrin Meissner and
Christian von Mering and
Heinz{-}Theodor Mevissen and
Hans{-}Werner Mewes and
Holger Michael and
Martin Mokrejs and
Tobias M{\"{u}}ller and
Heike Pospisil and
Matthias Rarey and
Jens G. Reich and
Ralf Schneider and
Dietmar Schomburg and
Steffen Schulze{-}Kremer and
Knut Schwarzer and
Ingolf Sommer and
Stephan Springstubbe and
S{\'{a}}ndor Suhai and
Gnanasekaran Thoppae and
Martin Vingron and
Jens Warfsmann and
Thomas Werner and
Daniel Wetzler and
Edgar Wingender and
Ralf Zimmer},
title = {The Helmholtz Network for Bioinformatics: an integrative web portal
for bioinformatics resources},
journal = {Bioinform.},
volume = {20},
number = {2},
pages = {268--270},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg398},
doi = {10.1093/BIOINFORMATICS/BTG398},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CrassAB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FrickerGR04,
author = {Patrick C. Fricker and
Marcus Gastreich and
Matthias Rarey},
title = {Automated Drawing of Structural Molecular Formulas under Constraints},
journal = {J. Chem. Inf. Model.},
volume = {44},
number = {3},
pages = {1065--1078},
year = {2004},
url = {https://doi.org/10.1021/ci049958u},
doi = {10.1021/CI049958U},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FrickerGR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HindleRBL02,
author = {Sally A. Hindle and
Matthias Rarey and
Christian Buning and
Thomas Lengauer},
title = {Flexible docking under pharmacophore type constraints},
journal = {J. Comput. Aided Mol. Des.},
volume = {16},
number = {2},
pages = {129--149},
year = {2002},
url = {https://doi.org/10.1023/A:1016399411208},
doi = {10.1023/A:1016399411208},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HindleRBL02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gi/Rarey02,
author = {Matthias Rarey},
editor = {Sigrid E. Schubert and
Bernd Reusch and
Norbert Jesse},
title = {Geometric Problems and Algorithms in Computer-Aided Molecular Design},
booktitle = {32. Jahrestagung der Gesellschaft f{\"{u}}r Informatik, Informatik
bewegt, {INFORMATIK} 2002, Dortmund, Germany, September 30 - October
3, 2002, Erg{\"{a}}nzungsband},
series = {{LNI}},
volume = {{P-20}},
pages = {61--62},
publisher = {{GI}},
year = {2002},
url = {https://dl.gi.de/handle/20.500.12116/30191},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gi/Rarey02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/daglib/0006512,
author = {Matthias Rarey},
title = {Algorithmen f{\"{u}}r den computergest{\"{u}}tzten Wirkstoffentwurf},
series = {{GMD} research series},
volume = {22},
publisher = {{GMD}},
year = {2001},
isbn = {978-3-88457-405-8},
timestamp = {Tue, 18 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/daglib/0006512.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RareyS01,
author = {Matthias Rarey and
Martin Stahl},
title = {Similarity searching in large combinatorial chemistry spaces},
journal = {J. Comput. Aided Mol. Des.},
volume = {15},
number = {6},
pages = {497--520},
year = {2001},
url = {https://doi.org/10.1023/A:1011144622059},
doi = {10.1023/A:1011144622059},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RareyS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RareyKL99,
author = {Matthias Rarey and
Bernd Kramer and
Thomas Lengauer},
title = {Docking of hydrophobic ligands with interaction-based matching algorithms},
journal = {Bioinform.},
volume = {15},
number = {3},
pages = {243--250},
year = {1999},
url = {https://doi.org/10.1093/bioinformatics/15.3.243},
doi = {10.1093/BIOINFORMATICS/15.3.243},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RareyKL99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RareyD98,
author = {Matthias Rarey and
J. Scott Dixon},
title = {Feature trees: {A} new molecular similarity measure based on tree
matching},
journal = {J. Comput. Aided Mol. Des.},
volume = {12},
number = {5},
pages = {471--490},
year = {1998},
url = {https://doi.org/10.1023/A:1008068904628},
doi = {10.1023/A:1008068904628},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RareyD98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/RareyKL98,
author = {Matthias Rarey and
Bernd Kramer and
Thomas Lengauer},
title = {Docking of hydrophobic ligands with interaction-based matching algorithms},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1998,
University of Cologne, Germany, October 1998},
publisher = {Oxford University Press},
year = {1998},
timestamp = {Fri, 02 Aug 2019 15:48:14 +0200},
biburl = {https://dblp.org/rec/conf/gcb/RareyKL98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RareyKL97,
author = {Matthias Rarey and
Bernd Kramer and
Thomas Lengauer},
title = {Multiple automatic base selection: Protein-ligand docking based on
incremental construction without manual intervention},
journal = {J. Comput. Aided Mol. Des.},
volume = {11},
number = {4},
pages = {369--384},
year = {1997},
url = {https://doi.org/10.1023/A:1007913026166},
doi = {10.1023/A:1007913026166},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RareyKL97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/daglib/0086777,
author = {Matthias Rarey},
title = {Rechnergest{\"{u}}tzte Vorhersage von Rezeptor-Ligand-Wechselwirkungen},
series = {GMD-Bericht},
volume = {268},
publisher = {Oldenbourg},
year = {1996},
isbn = {978-3-486-24010-8},
timestamp = {Fri, 19 Jul 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/daglib/0086777.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RareyWL96,
author = {Matthias Rarey and
Stephan Wefing and
Thomas Lengauer},
title = {Placement of medium-sized molecular fragments into active sites of
proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {10},
number = {1},
pages = {41--54},
year = {1996},
url = {https://doi.org/10.1007/BF00124464},
doi = {10.1007/BF00124464},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RareyWL96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/RareyKL95,
author = {Matthias Rarey and
Bernd Kramer and
Thomas Lengauer},
editor = {Christopher J. Rawlings and
Dominic A. Clark and
Russ B. Altman and
Lawrence Hunter and
Thomas Lengauer and
Shoshana J. Wodak},
title = {Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins},
booktitle = {Proceedings of the Third International Conference on Intelligent Systems
for Molecular Biology, Cambridge, United Kingdom, July 16-19, 1995},
pages = {300--308},
publisher = {{AAAI}},
year = {1995},
url = {http://www.aaai.org/Library/ISMB/1995/ismb95-036.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/RareyKL95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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