Literature DB >> 16231203

Virtual computational chemistry laboratory--design and description.

Igor V Tetko1, Johann Gasteiger, Roberto Todeschini, Andrea Mauri, David Livingstone, Peter Ertl, Vladimir A Palyulin, Eugene V Radchenko, Nikolay S Zefirov, Alexander S Makarenko, Vsevolod Yu Tanchuk, Volodymyr V Prokopenko.   

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.

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Year:  2005        PMID: 16231203     DOI: 10.1007/s10822-005-8694-y

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  15 in total

1.  Unsupervised forward selection: a method for eliminating redundant variables.

Authors:  D C Whitley; M G Ford; D J Livingstone
Journal:  J Chem Inf Comput Sci       Date:  2000 Sep-Oct

2.  Estimation of aqueous solubility of chemical compounds using E-state indices.

Authors:  I V Tetko; V Y Tanchuk; T N Kasheva; A E Villa
Journal:  J Chem Inf Comput Sci       Date:  2001 Nov-Dec

3.  Prediction of n-octanol/water partition coefficients from PHYSPROP database using artificial neural networks and E-state indices.

Authors:  I V Tetko; V Y Tanchuk; A E Villa
Journal:  J Chem Inf Comput Sci       Date:  2001 Sep-Oct

4.  Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program.

Authors:  Igor V Tetko; Vsevolod Yu Tanchuk
Journal:  J Chem Inf Comput Sci       Date:  2002 Sep-Oct

5.  Neural network studies. 4. Introduction to associative neural networks.

Authors:  Igor V Tetko
Journal:  J Chem Inf Comput Sci       Date:  2002 May-Jun

6.  Distant collaboration in drug discovery: the LINK3D project.

Authors:  Manuel Pastor; Paolo Benedetti; Angelo Carotti; Antonio Carrieri; Carlos Díaz; Cristina Herráiz; Hans-Dieter Höltje; M Isabel Loza; Tudor Oprea; Fernando Padín; Francesc Pubill; Ferran Sanz; Friederike Stoll
Journal:  J Comput Aided Mol Des       Date:  2002-11       Impact factor: 3.686

7.  Representation and use of chemistry in the global electronic age.

Authors:  Peter Murray-Rust; Henry S Rzepa; Simon M Tyrrell; Yong Zhang
Journal:  Org Biomol Chem       Date:  2004-10-22       Impact factor: 3.876

8.  Application of ALOGPS to predict 1-octanol/water distribution coefficients, logP, and logD, of AstraZeneca in-house database.

Authors:  Igor V Tetko; Pierre Bruneau
Journal:  J Pharm Sci       Date:  2004-12       Impact factor: 3.534

9.  Application of ALOGPS 2.1 to predict log D distribution coefficient for Pfizer proprietary compounds.

Authors:  Igor V Tetko; Gennadiy I Poda
Journal:  J Med Chem       Date:  2004-11-04       Impact factor: 7.446

10.  Atom/fragment contribution method for estimating octanol-water partition coefficients.

Authors:  W M Meylan; P H Howard
Journal:  J Pharm Sci       Date:  1995-01       Impact factor: 3.534

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  248 in total

1.  The perspectives of computational chemistry modeling.

Authors:  Igor V Tetko
Journal:  J Comput Aided Mol Des       Date:  2011-12-11       Impact factor: 3.686

2.  Automatic formation of hypotheses on the relationships between structure of naphthalene analogs and bioluminescence response of bioreporter Pseudomonas fluorescens HK44.

Authors:  J Trögl; J Hálová; G Kuncová; P Pařík
Journal:  Folia Microbiol (Praha)       Date:  2010-10-13       Impact factor: 2.099

3.  QSAR studies for prediction of cross-β sheet aggregate binding affinity and selectivity.

Authors:  Katryna Cisek; Jeff Kuret
Journal:  Bioorg Med Chem       Date:  2012-01-12       Impact factor: 3.641

4.  Estimating n-octanol-water partition coefficients for neutral highly hydrophobic chemicals using measured n-butanol-water partition coefficients.

Authors:  Kaila B Hanson; Dale J Hoff; Tylor J Lahren; David R Mount; Anthony J Squillace; Lawrence P Burkhard
Journal:  Chemosphere       Date:  2018-11-24       Impact factor: 7.086

5.  MALDI Mass Spectrometry Imaging Reveals Heterogeneous Distribution of Tenofovir and Tenofovir Diphosphate in Colorectal Tissue of Subjects Receiving a Tenofovir-Containing Enema.

Authors:  Herana Kamal Seneviratne; Craig W Hendrix; Edward J Fuchs; Namandjé N Bumpus
Journal:  J Pharmacol Exp Ther       Date:  2018-07-23       Impact factor: 4.030

6.  Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors.

Authors:  Preyesh Stephen; Ramachandran Vijayan; Audesh Bhat; N Subbarao; R N K Bamezai
Journal:  J Comput Aided Mol Des       Date:  2007-08-21       Impact factor: 3.686

7.  Outer Membrane Vesicles Facilitate Trafficking of the Hydrophobic Signaling Molecule CAI-1 between Vibrio harveyi Cells.

Authors:  Sophie Brameyer; Laure Plener; Axel Müller; Andreas Klingl; Gerhard Wanner; Kirsten Jung
Journal:  J Bacteriol       Date:  2018-07-10       Impact factor: 3.490

8.  Constrained Photophysics of 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one in the Bioenvironment of Serum Albumins: A Spectroscopic Endeavour Supported by Molecular Docking Analysis.

Authors:  Amrit Krishna Mitra; Abhishek Sau; Uttam Pal; Chandan Saha; Samita Basu
Journal:  J Fluoresc       Date:  2017-04-22       Impact factor: 2.217

9.  FE(II) is the native cofactor for Escherichia coli methionine aminopeptidase.

Authors:  Sergio C Chai; Wen-Long Wang; Qi-Zhuang Ye
Journal:  J Biol Chem       Date:  2008-07-31       Impact factor: 5.157

10.  New benzenesulphonohydrazide derivatives as potential antitumour agents.

Authors:  Łukasz Popiołek; Monika Gawrońska-Grzywacz; Anna Berecka-Rycerz; Kinga Paruch; Iwona Piątkowska-Chmiel; Dorota Natorska-Chomicka; Mariola Herbet; Anna Gumieniczek; Jarosław Dudka; Monika Wujec
Journal:  Oncol Lett       Date:  2020-09-02       Impact factor: 2.967

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