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ORCIDBibTeX records: Michael Feig
@article{DBLP:journals/ploscb/DutagaciDQKF23,
author = {Bercem Dutagaci and
Bingbing Duan and
Chenxi Qiu and
Craig D. Kaplan and
Michael Feig},
title = {Characterization of {RNA} polymerase {II} trigger loop mutations using
molecular dynamics simulations and machine learning},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {3},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1010999},
doi = {10.1371/JOURNAL.PCBI.1010999},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DutagaciDQKF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/OstrowskaFT23,
author = {Natalia Ostrowska and
Michael Feig and
Joanna Trylska},
title = {Varying molecular interactions explain aspects of crowder-dependent
enzyme function of a viral protease},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {4},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1011054},
doi = {10.1371/JOURNAL.PCBI.1011054},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/OstrowskaFT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/JungKKTKMINIIFS21,
author = {Jaewoon Jung and
Chigusa Kobayashi and
Kento Kasahara and
Cheng Tan and
Akiyoshi Kuroda and
Kazuo Minami and
Shigeru Ishiduki and
Tatsuo Nishiki and
Hikaru Inoue and
Yutaka Ishikawa and
Michael Feig and
Yuji Sugita},
title = {New parallel computing algorithm of molecular dynamics for extremely
huge scale biological systems},
journal = {J. Comput. Chem.},
volume = {42},
number = {4},
pages = {231--241},
year = {2021},
url = {https://doi.org/10.1002/jcc.26450},
doi = {10.1002/JCC.26450},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/JungKKTKMINIIFS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/GongCLNFBC20,
author = {Xiping Gong and
Mara Chiricotto and
Xiaorong Liu and
Erik B. Nordquist and
Michael Feig and
Charles L. Brooks III and
Jianhan Chen},
title = {Accelerating the Generalized Born with Molecular Volume and Solvent
Accessible Surface Area Implicit Solvent Model Using Graphics Processing
Units},
journal = {J. Comput. Chem.},
volume = {41},
number = {8},
pages = {830--838},
year = {2020},
url = {https://doi.org/10.1002/jcc.26133},
doi = {10.1002/JCC.26133},
timestamp = {Thu, 14 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/GongCLNFBC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BrockeDMDF19,
author = {Stephanie A. Brocke and
Alexandra Degen and
Alexander D. MacKerell Jr. and
Bercem Dutagaci and
Michael Feig},
title = {Prediction of Membrane Permeation of Drug Molecules by Combining an
Implicit Membrane Model with Machine Learning},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {3},
pages = {1147--1162},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00648},
doi = {10.1021/ACS.JCIM.8B00648},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BrockeDMDF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeoF18,
author = {Lim Heo and
Michael Feig},
title = {{PREFMD:} a web server for protein structure refinement via molecular
dynamics simulations},
journal = {Bioinform.},
volume = {34},
number = {6},
pages = {1063--1065},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx726},
doi = {10.1093/BIOINFORMATICS/BTX726},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeoF18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/DutagaciSF17,
author = {Bercem Dutagaci and
Maryam Sayadi and
Michael Feig},
title = {Heterogeneous dielectric generalized Born model with a van der Waals
term provides improved association energetics of membrane-embedded
transmembrane helices},
journal = {J. Comput. Chem.},
volume = {38},
number = {16},
pages = {1308--1320},
year = {2017},
url = {https://doi.org/10.1002/jcc.24691},
doi = {10.1002/JCC.24691},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/DutagaciSF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DutagaciF17,
author = {Bercem Dutagaci and
Michael Feig},
title = {Determination of Hydrophobic Lengths of Membrane Proteins with the
{HDGB} Implicit Membrane Model},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {12},
pages = {3032--3042},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00510},
doi = {10.1021/ACS.JCIM.7B00510},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/DutagaciF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Feig16,
author = {Michael Feig},
title = {Local Protein Structure Refinement via Molecular Dynamics Simulations
with locPREFMD},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {7},
pages = {1304--1312},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.6b00222},
doi = {10.1021/ACS.JCIM.6B00222},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/Feig16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WangFSLPF16,
author = {Beibei Wang and
Joshua Francis and
Monika Sharma and
Sean M. Law and
Alexander V. Predeus and
Michael Feig},
title = {Long-Range Signaling in MutS and {MSH} Homologs via Switching of Dynamic
Communication Pathways},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {10},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1005159},
doi = {10.1371/JOURNAL.PCBI.1005159},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WangFSLPF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ChengGLF12,
author = {Yi{-}Ming Cheng and
Srinivasa Murthy Gopal and
Sean M. Law and
Michael Feig},
title = {Molecular Dynamics Trajectory Compression with a Coarse-Grained Model},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {2},
pages = {476--486},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2011.141},
doi = {10.1109/TCBB.2011.141},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ChengGLF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZavodszkySLF09,
author = {Maria I. Zavodszky and
Andrew W. Stumpff{-}Kane and
David J. Lee and
Michael Feig},
title = {Scoring confidence index: statistical evaluation of ligand binding
mode predictions},
journal = {J. Comput. Aided Mol. Des.},
volume = {23},
number = {5},
pages = {289--299},
year = {2009},
url = {https://doi.org/10.1007/s10822-008-9258-8},
doi = {10.1007/S10822-008-9258-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZavodszkySLF09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/BrooksBMNPRWABBCCCDFFGHIKLMOPPPPSTVWWYYK09,
author = {Bernard R. Brooks and
Charles L. Brooks III and
Alexander D. MacKerell Jr. and
Lennart Nilsson and
Robert J. Petrella and
Beno{\^{\i}}t Roux and
Y. Won and
G. Archontis and
Christian Bartels and
Stefan Boresch and
Amedeo Caflisch and
Leo S. D. Caves and
Qiang Cui and
Aaron R. Dinner and
Michael Feig and
S. Fischer and
Jiali Gao and
Milan Hodoscek and
Wonpil Im and
Krzysztof Kuczera and
Themis Lazaridis and
J. Ma and
Victor Ovchinnikov and
Emanuele Paci and
Richard W. Pastor and
C. B. Post and
J. Z. Pu and
Michael Schaefer and
Bruce Tidor and
Richard M. Venable and
H. Lee Woodcock III and
X. Wu and
W. Yang and
Darrin M. York and
Martin Karplus},
title = {{CHARMM:} The biomolecular simulation program},
journal = {J. Comput. Chem.},
volume = {30},
number = {10},
pages = {1545--1614},
year = {2009},
url = {https://doi.org/10.1002/jcc.21287},
doi = {10.1002/JCC.21287},
timestamp = {Thu, 08 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/BrooksBMNPRWABBCCCDFFGHIKLMOPPPPSTVWWYYK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/ZhouFW08,
author = {Yongcheng Zhou and
Michael Feig and
Guo{-}Wei Wei},
title = {Highly accurate biomolecular electrostatics in continuum dielectric
environments},
journal = {J. Comput. Chem.},
volume = {29},
number = {1},
pages = {87--97},
year = {2008},
url = {https://doi.org/10.1002/jcc.20769},
doi = {10.1002/JCC.20769},
timestamp = {Thu, 04 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/ZhouFW08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/WittayanarakulHF08,
author = {Kitiyaporn Wittayanarakul and
Supot Hannongbua and
Michael Feig},
title = {Accurate prediction of protonation state as a prerequisite for reliable
{MM-PB(GB)SA} binding free energy calculations of {HIV-1} protease
inhibitors},
journal = {J. Comput. Chem.},
volume = {29},
number = {5},
pages = {673--685},
year = {2008},
url = {https://doi.org/10.1002/jcc.20821},
doi = {10.1002/JCC.20821},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/WittayanarakulHF08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/OlsonFB08,
author = {Mark A. Olson and
Michael Feig and
Charles L. Brooks III},
title = {Prediction of protein loop conformations using multiscale modeling
methods with physical energy scoring functions},
journal = {J. Comput. Chem.},
volume = {29},
number = {5},
pages = {820--831},
year = {2008},
url = {https://doi.org/10.1002/jcc.20827},
doi = {10.1002/JCC.20827},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/OlsonFB08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WittayanarakulHF07,
author = {Kitiyaporn Wittayanarakul and
Supot Hannongbua and
Michael Feig},
title = {On the correlation between drug-resistant pattern of {HIV-1} protease
inhibitors and binding free energy and structural changes},
journal = {{BMC} Syst. Biol.},
volume = {1},
number = {{S-1}},
pages = {P58},
year = {2007},
url = {https://doi.org/10.1186/1752-0509-1-S1-P58},
doi = {10.1186/1752-0509-1-S1-P58},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/WittayanarakulHF07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/ChocholousovaF06,
author = {Jana Chocholousov{\'{a}} and
Michael Feig},
title = {Balancing an accurate representation of the molecular surface in generalized
born formalisms with integrator stability in molecular dynamics simulations},
journal = {J. Comput. Chem.},
volume = {27},
number = {6},
pages = {719--729},
year = {2006},
url = {https://doi.org/10.1002/jcc.20387},
doi = {10.1002/JCC.20387},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/ChocholousovaF06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcphy/ZhouZFW06,
author = {Yongcheng Zhou and
Shan Zhao and
Michael Feig and
Guo{-}Wei Wei},
title = {High order matched interface and boundary method for elliptic equations
with discontinuous coefficients and singular sources},
journal = {J. Comput. Phys.},
volume = {213},
number = {1},
pages = {1--30},
year = {2006},
url = {https://doi.org/10.1016/j.jcp.2005.07.022},
doi = {10.1016/J.JCP.2005.07.022},
timestamp = {Wed, 03 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcphy/ZhouZFW06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/FeigOLICB04,
author = {Michael Feig and
Alexey Onufriev and
Michael S. Lee and
Wonpil Im and
David A. Case and
Charles L. Brooks III},
title = {Performance comparison of generalized born and Poisson methods in
the calculation of electrostatic solvation energies for protein structures},
journal = {J. Comput. Chem.},
volume = {25},
number = {2},
pages = {265--284},
year = {2004},
url = {https://doi.org/10.1002/jcc.10378},
doi = {10.1002/JCC.10378},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/FeigOLICB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/MackerellFB04,
author = {Alexander D. MacKerell Jr. and
Michael Feig and
Charles L. Brooks III},
title = {Extending the treatment of backbone energetics in protein force fields:
Limitations of gas-phase quantum mechanics in reproducing protein
conformational distributions in molecular dynamics simulations},
journal = {J. Comput. Chem.},
volume = {25},
number = {11},
pages = {1400--1415},
year = {2004},
url = {https://doi.org/10.1002/jcc.20065},
doi = {10.1002/JCC.20065},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/MackerellFB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/LeeFSB03,
author = {Michael S. Lee and
Michael Feig and
Freddie R. Salsbury Jr. and
Charles L. Brooks III},
title = {New analytic approximation to the standard molecular volume definition
and its application to generalized Born calculations},
journal = {J. Comput. Chem.},
volume = {24},
number = {11},
pages = {1348--1356},
year = {2003},
url = {https://doi.org/10.1002/jcc.10272},
doi = {10.1002/JCC.10272},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/LeeFSB03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/LeeFSB03a,
author = {Michael S. Lee and
Michael Feig and
Freddie R. Salsbury Jr. and
Charles L. Brooks III},
title = {New analytic approximation to the standard molecular volume definition
and its application to generalized born calculations - Erratum},
journal = {J. Comput. Chem.},
volume = {24},
number = {14},
pages = {1821},
year = {2003},
url = {https://doi.org/10.1002/jcc.10367},
doi = {10.1002/JCC.10367},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/LeeFSB03a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fgcs/FeigAJP99,
author = {Michael Feig and
Matin Abdullah and
S. Lennart Johnsson and
B. Montgomery Pettitt},
title = {Large scale distributed data repository: design of a molecular dynamics
trajectory database},
journal = {Future Gener. Comput. Syst.},
volume = {16},
number = {1},
pages = {101--110},
year = {1999},
url = {https://doi.org/10.1016/S0167-739X(99)00039-4},
doi = {10.1016/S0167-739X(99)00039-4},
timestamp = {Wed, 19 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fgcs/FeigAJP99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ppl/LarssonFJ99,
author = {Olle Larsson and
Michael Feig and
S. Lennart Johnsson},
title = {Some Metacomputing Experiences for Scientific Applications},
journal = {Parallel Process. Lett.},
volume = {9},
number = {2},
pages = {243--252},
year = {1999},
url = {https://doi.org/10.1142/S0129626499000232},
doi = {10.1142/S0129626499000232},
timestamp = {Tue, 24 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ppl/LarssonFJ99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/daglib/0082241,
author = {Michael Feig},
title = {Einf{\"{u}}hrung in {GNU}},
series = {{UNIX} easy},
publisher = {Hanser},
year = {1996},
isbn = {978-3-446-18311-7},
timestamp = {Tue, 12 Apr 2011 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/daglib/0082241.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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