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ORCIDJournal of Cheminformatics, Volume 3
Volume 3, 2011
- Axel Drefahl
:
CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. 1
- Michael P. Mazanetz, Osamu Ichihara, Richard Law, Mark Whittaker:
Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method. 2 - Georg Hinselmann, Lars Rosenbaum, Andreas Jahn, Nikolas Fechner, Andreas Zell:
jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints. 3 - Evan Bolton, Sunghwan Kim, Stephen H. Bryant:
PubChem3D: Conformer generation. 4 - Andrei A. Gakh, Michael N. Burnett, Sergei V. Trepalin, Alexander V. Yarkov:
Modular Chemical Descriptor Language (MCDL): Stereochemical modules. 5 - Pavel Dallakian, Norbert Haider:
FlaME: Flash Molecular Editor - a 2D structure input tool for the web. 6 - Norman C. LeDonne, Kevin Rissolo, James Bulgarelli, Leonard Tini:
Use of structure-activity landscape index curves and curve integrals to evaluate the performance of multiple machine learning prediction models. 7 - Noel M. O'Boyle, Tim Vandermeersch, Christopher J. Flynn, Anita R. Maguire, Geoffrey R. Hutchison:
Confab - Systematic generation of diverse low-energy conformers. 8 - Evan Bolton, Sunghwan Kim, Stephen H. Bryant:
PubChem3D: Diversity of shape. 9 - Noel M. O'Boyle:
Review of "Data Analysis with Open Source Tools" by Philipp K Janert. 10 - Lars Rosenbaum, Georg Hinselmann, Andreas Jahn, Andreas Zell:
Interpreting linear support vector machine models with heat map molecule coloring. 11 - Andrew P. Norgan, Paul K. Coffman, Jean-Pierre A. Kocher, David J. Katzmann, Carlos P. Sosa:
Multilevel Parallelization of AutoDock 4.2. 12 - Evan Bolton, Sunghwan Kim, Stephen H. Bryant:
PubChem3D: Similar conformers. 13 - Christopher Southan, Kiran Boppana, Sarma A. R. P. Jagarlapudi, Sorel Muresan:
Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds. 14 - Egon L. Willighagen, Martin P. Brändle:
Resource description framework technologies in chemistry. 15 - Leonid L. Chepelev, Michel Dumontier:
Semantic Web integration of Cheminformatics resources with the SADI framework. 16 - Lezan Hawizy, David M. Jessop, Nico Adams, Peter Murray-Rust:
ChemicalTagger: A tool for semantic text-mining in chemistry. 17 - Nina Jeliazkova, Vedrin Jeliazkov:
AMBIT RESTful web services: an implementation of the OpenTox application programming interface. 18 - Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Kallesøe, Egon L. Willighagen, Janos G. Hajagos, M. Scott Marshall, Eric Prud'hommeaux, Oktie Hassanzadeh, Elgar Pichler, Susie Stephens:
Linked open drug data for pharmaceutical research and development. 19 - Leonid L. Chepelev, Michel Dumontier:
Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. 20 - Katrin Stierand, Matthias Rarey:
Consistent two-dimensional visualization of protein-ligand complex series. 21 - Fabian Buchwald, Lothar Richter, Stefan Kramer:
Predicting a small molecule-kinase interaction map: A machine learning approach. 22 - Andreas Jahn, Lars Rosenbaum, Georg Hinselmann, Andreas Zell:
4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening. 23 - Xin Fu, Anna Wojak, Daniel Neagu, Mick J. Ridley, Kim Travis:
Data governance in predictive toxicology: A review. 24 - Sunghwan Kim, Evan Bolton, Stephen H. Bryant:
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles. 25 - Sunghwan Kim, Evan Bolton, Stephen H. Bryant:
PubChem3D: Biologically relevant 3-D similarity. 26 - Jochen Junker:
Theoretical NMR correlations based Structure Discussion. 27 - Jonna C. Stålring, Lars Carlsson, Pedro Almeida, Scott Boyer:
AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment. 28 - John D. Holliday, Evangelos Kanoulas, Nurul Malim, Peter Willett:
Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision. 29 - Varun Khanna, Shoba Ranganathan:
Structural diversity of biologically interesting datasets: a scaffold analysis approach. 30 - Jochen Junker:
Statistical filtering for NMR based structure generation. 31 - Evan Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A. Thiessen, Jiyao Wang, Bo Yu, Jian Zhang, Stephen H. Bryant:
PubChem3D: a new resource for scientists. 32 - Noel M. O'Boyle, Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch, Geoffrey R. Hutchison:
Open Babel: An open chemical toolbox. 33 - Dan W. Zaharevitz:
Adventures in public data. 34 - Cameron Neylon:
Three stories about the conduct of science: Past, future, and present. 35 - John Wilbanks:
Openness as infrastructure. 36 - Noel M. O'Boyle, Rajarshi Guha, Egon L. Willighagen, Sam E. Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V. Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Andrew S. I. D. Lang, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jérôme Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, Peter Murray-Rust:
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. 37 - Sam E. Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D. Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas, Joe Townsend:
The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age. 38 - Joe Townsend, Peter Murray-Rust:
CMLLite: a design philosophy for CML. 39 - David M. Jessop, Sam E. Adams, Peter Murray-Rust:
Mining chemical information from open patents. 40 - David M. Jessop, Sam E. Adams, Egon L. Willighagen, Lezan Hawizy, Peter Murray-Rust:
OSCAR4: a flexible architecture for chemical text-mining. 41 - Peter Murray-Rust, Sam E. Adams, Jim Downing, Joe Townsend, Yong Zhang:
The semantic architecture of the World-Wide Molecular Matrix (WWMM). 42 - Peter Murray-Rust, Joe Townsend, Sam E. Adams, Weerapong Phadungsukanan, Jens Thomas:
The semantics of Chemical Markup Language (CML): dictionaries and conventions. 43 - Peter Murray-Rust, Henry S. Rzepa:
CML: Evolution and design. 44 - Brian Brooks, Adam L. Thorn, Matthew Smith, Peter Matthews, Shaoming Chen, Ben O'Steen, Sam E. Adams, Joe Townsend, Peter Murray-Rust:
Ami - The chemist's amanuensis. 45 - Henry S. Rzepa:
The past, present and future of Scientific discourse. 46 - Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O'Steen, William Waites:
Open Bibliography for Science, Technology, and Medicine. 47 - Peter Murray-Rust:
Semantic science and its communication - a personal view. 48 - Abrar Hussain, Peter E. Shaw, Jonathan D. Hirst:
Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain. 49 - Tsutomu Osoda, Satoru Miyano:
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. 50 - Patrick McCarren, Clayton Springer, Lewis Whitehead:
An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential. 51 - Jun D. Zhang, Lewis Y. Geer, Evan Bolton, Stephen H. Bryant:
Automated annotation of chemical names in the literature with tunable accuracy. 52 - Jörg-Hubertus Wilhelm:
MyChemise: A 2D drawing program that uses morphing for visualisation purposes. 53 - Andreas Truszkowski, Kalai Vanii Jayaseelan, Stefan Neumann, Egon L. Willighagen, Achim Zielesny, Christoph Steinbeck:
New developments on the cheminformatics open workflow environment CDK-Taverna. 54
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