Literature DB >> 9190290

A new class of models for computing receptor-ligand binding affinities.

M K Gilson1, J A Given, M S Head.   

Abstract

Models for predicting the binding affinities of molecules in solution are either very detailed, making them computationally intensive and hard to test, or very simple, and thus less informative than one might wish. A new class of models that focus on the predominant states of the binding molecules promise to capture the essential physics of binding at modest computational cost.

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Year:  1997        PMID: 9190290     DOI: 10.1016/s1074-5521(97)90251-9

Source DB:  PubMed          Journal:  Chem Biol        ISSN: 1074-5521


  17 in total

1.  Scoring functions: a view from the bench.

Authors:  J R Tame
Journal:  J Comput Aided Mol Des       Date:  1999-03       Impact factor: 3.686

2.  The effect of multiple binding modes on empirical modeling of ligand docking to proteins.

Authors:  R Brem; K A Dill
Journal:  Protein Sci       Date:  1999-05       Impact factor: 6.725

3.  Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design.

Authors:  Wei Chen; Chia-En Chang; Michael K Gilson
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

4.  Structural determinants of trypsin affinity and specificity for cationic inhibitors.

Authors:  F Polticelli; P Ascenzi; M Bolognesi; B Honig
Journal:  Protein Sci       Date:  1999-12       Impact factor: 6.725

5.  Calculation of absolute protein-ligand binding affinity using path and endpoint approaches.

Authors:  Michael S Lee; Mark A Olson
Journal:  Biophys J       Date:  2005-11-11       Impact factor: 4.033

6.  Molecular motions in drug design: the coming age of the metadynamics method.

Authors:  Xevi Biarnés; Salvatore Bongarzone; Attilio Vittorio Vargiu; Paolo Carloni; Paolo Ruggerone
Journal:  J Comput Aided Mol Des       Date:  2011-02-17       Impact factor: 3.686

7.  Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

Authors:  E V Katkova; A V Onufriev; B Aguilar; V B Sulimov
Journal:  J Mol Graph Model       Date:  2016-12-21       Impact factor: 2.518

Review 8.  Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.

Authors:  Jeff Wereszczynski; J Andrew McCammon
Journal:  Q Rev Biophys       Date:  2011-11-15       Impact factor: 5.318

9.  Path-integral method for predicting relative binding affinities of protein-ligand complexes.

Authors:  Chandrika Mulakala; Yiannis N Kaznessis
Journal:  J Am Chem Soc       Date:  2009-04-01       Impact factor: 15.419

Review 10.  Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.

Authors:  Ahmet Bakan; John S Lazo; Peter Wipf; Kay M Brummond; Ivet Bahar
Journal:  Curr Med Chem       Date:  2008       Impact factor: 4.530

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