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Journal 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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