Literature DB >> 18232647

Robust classification of "relevant" water molecules in putative protein binding sites.

Alessio Amadasi1, J Andrew Surface, Francesca Spyrakis, Pietro Cozzini, Andrea Mozzarelli, Glen E Kellogg.   

Abstract

A statistically validated protocol to identify "relevant" water molecules in protein binding sites using HINT score and a geometric descriptor termed Rank is described. In training, conservation/nonconservation was modeled for 86% of the waters. For the test set, 87% of waters were correctly classified (92% when crystallographic resolution was <or=2.0 A). Conserved waters make at least two hydrogen bonds with protein and gain 0.6-2.0 kcal mol(-1) more binding energy than nonconserved waters.

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Year:  2008        PMID： 18232647     DOI： 10.1021/jm701023h

Source DB:  PubMed          Journal:  J Med Chem        ISSN： 0022-2623            Impact factor:   7.446


  20 in total

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Journal:  J Med Chem       Date:  2012-01-13       Impact factor: 7.446

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Journal:  J Med Chem       Date:  2020-10-02       Impact factor: 7.446

Review 3.  A medicinal chemist's guide to molecular interactions.

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Journal:  J Med Chem       Date:  2010-07-22       Impact factor: 7.446

4.  Design of O-acetylserine sulfhydrylase inhibitors by mimicking nature.

Authors:  Enea Salsi; Alexander S Bayden; Francesca Spyrakis; Alessio Amadasi; Barbara Campanini; Stefano Bettati; Tetyana Dodatko; Pietro Cozzini; Glen E Kellogg; Paul F Cook; Steven L Roderick; Andrea Mozzarelli
Journal:  J Med Chem       Date:  2010-01-14       Impact factor: 7.446

Review 5.  Hydrophobicity--shake flasks, protein folding and drug discovery.

Authors:  Aurijit Sarkar; Glen E Kellogg
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6.  Computational study of EGFR inhibition: molecular dynamics studies on the active and inactive protein conformations.

Authors:  Napat Songtawee; M Paul Gleeson; Kiattawee Choowongkomon
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7.  Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT.

Authors:  Alexander S Bayden; Micaela Fornabaio; J Neel Scarsdale; Glen E Kellogg
Journal:  J Comput Aided Mol Des       Date:  2009-06-25       Impact factor: 3.686

8.  Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif.

Authors:  Mostafa H Ahmed; Francesca Spyrakis; Pietro Cozzini; Parijat K Tripathi; Andrea Mozzarelli; J Neel Scarsdale; Martin A Safo; Glen E Kellogg
Journal:  PLoS One       Date:  2011-09-22       Impact factor: 3.240

9.  Rationalizing tight ligand binding through cooperative interaction networks.

Authors:  Bernd Kuhn; Julian E Fuchs; Michael Reutlinger; Martin Stahl; Neil R Taylor
Journal:  J Chem Inf Model       Date:  2011-12-09       Impact factor: 4.956

10.  On the specificity of heparin/heparan sulfate binding to proteins. Anion-binding sites on antithrombin and thrombin are fundamentally different.

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Journal:  PLoS One       Date:  2012-11-12       Impact factor: 3.240
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