Journal ArticleDOI
Virtual computational chemistry laboratory - design and description
Igor V. Tetko,Johann Gasteiger,Roberto Todeschini,Andrea Mauri,David J. Livingstone,Peter Ertl,Vladimir A. Palyulin,Eugene V. Radchenko,Nikolai S. Zefirov,Alexander S. Makarenko,Vsevolod Yu. Tanchuk,Volodymyr V. Prokopenko +11 more
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TLDR
The main features and statistics of the developed system, Virtual Computational Chemistry Laboratory, allowing the computational chemist to perform a comprehensive series of molecular indices/properties calculations and data analysis are reviewed.Abstract:
Internet technology offers an excellent opportunity for the development of tools by the cooperative effort of various groups and institutions. We have developed a multi-platform software system, Virtual Computational Chemistry Laboratory, http://www.vcclab.org, allowing the computational chemist to perform a comprehensive series of molecular indices/properties calculations and data analysis. The implemented software is based on a three-tier architecture that is one of the standard technologies to provide client-server services on the Internet. The developed software includes several popular programs, including the indices generation program, DRAGON, a 3D structure generator, CORINA, a program to predict lipophilicity and aqueous solubility of chemicals, ALOGPS and others. All these programs are running at the host institutes located in five countries over Europe. In this article we review the main features and statistics of the developed system that can be used as a prototype for academic and industry models.read more
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Open Babel: An open chemical toolbox
Noel M. O'Boyle,Michael Banck,Craig A. James,Chris Morley,Tim Vandermeersch,Geoffrey R. Hutchison +5 more
TL;DR: The implementation of Open Babel is detailed, key advances in the 2.3 release are described, and a variety of uses are outlined both in terms of software products and scientific research, including applications far beyond simple format interconversion.
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ZINC: A Free Tool to Discover Chemistry for Biology
TL;DR: The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets and is freely available at zinc.docking.org.
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A semiempirical free energy force field with charge-based desolvation.
TL;DR: The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid‐based docking methods based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding.
Software News and Update A Semiempirical Free Energy Force Field with Charge-Based Desolvation
TL;DR: In this article, a semi-empirical free energy force field for use in AutoDock4 and similar grid-based docking methods is presented, based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding.
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Chiral recognition by enantioselective liquid chromatography: Mechanisms and modern chiral stationary phases
TL;DR: This tutorial review is mainly focused on mechanisms of chiral recognition and enantiomer distinction of popular chiral selectors and corresponding chiral stationary phases and attempts to provide the reader with vivid images of molecular recognition mechanisms of selected chiral selector-selectand pairs on basis of solid-state X-ray crystal structures and simulated computer models.
References
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Book
Handbook of Molecular Descriptors
TL;DR: This Users guide notations acronyms list of molecular descriptors contains abbreviations for molecular descriptor values that are useful for counting and topological descriptors calculation.
Journal ArticleDOI
Atom/fragment contribution method for estimating octanol-water partition coefficients
TL;DR: Atom/fragment contribution values, used to estimate the log octanol-water partition coefficient (log P) of organic compounds, have been determined for 130 simple chemical substructures by a multiple linear regression of 1120 compounds with measured log P values.
Journal ArticleDOI
The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics
Christoph Steinbeck,Yongquan Han,Stefan Kuhn,Oliver Horlacher,Edgar Luttmann,Egon Willighagen +5 more
TL;DR: The Chemistry Development Kit provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc.
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Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
TL;DR: Six currently available programs for automatic 3D structure generation were compared by converting the connectivity tables including appropriate stereodescriptors from this dataset of 639 molecular structures into 3D geometries: CONCORD, ALCOGEN, Chem-X, MOLGEO, COBRA, and CORINA.
Journal ArticleDOI
Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program.
TL;DR: This article provides a systematic study of several important parameters of the Associative Neural Network, such as the number of networks in the ensemble, distance measures, neighbor functions, selection of smoothing parameters, and strategies for the user-training feature of the algorithm.