Literature DB >> 9131247

Structure-based drug design: computational advances.

T J Marrone1, J M Briggs, J A McCammon.   

Abstract

Structure-based computational methods continue to enhance progress in the discovery and refinement of therapeutic agents. Several such methods and their applications are described. These include molecular visualization and molecular modeling, docking, fragment methods, 3-D database techniques, and free-energy perturbation. Related issues that are discussed include the use of simplified potential energy functions and the determination of the positions of tightly bound waters. Strengths and weaknesses of the various methods are described.

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Year:  1997        PMID: 9131247     DOI: 10.1146/annurev.pharmtox.37.1.71

Source DB:  PubMed          Journal:  Annu Rev Pharmacol Toxicol        ISSN: 0362-1642            Impact factor:   13.820


  26 in total

1.  Protein ligand docking based on empirical method for binding affinity estimation.

Authors:  P Tao; L Lai
Journal:  J Comput Aided Mol Des       Date:  2001-05       Impact factor: 3.686

2.  Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space.

Authors:  Richard M Jackson
Journal:  J Comput Aided Mol Des       Date:  2002-01       Impact factor: 3.686

3.  The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models.

Authors:  David G Lloyd; Alfonso T García-Sosa; Ian L Alberts; Nikolay P Todorov; Ricardo L Manceral
Journal:  J Comput Aided Mol Des       Date:  2004-02       Impact factor: 3.686

4.  Designing the molecular future.

Authors:  Gisbert Schneider
Journal:  J Comput Aided Mol Des       Date:  2011-11-30       Impact factor: 3.686

5.  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

6.  A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist.

Authors:  Nidhi Singh; Gwénaël Chevé; David M Ferguson; Christopher R McCurdy
Journal:  J Comput Aided Mol Des       Date:  2006-09-29       Impact factor: 3.686

7.  The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.

Authors:  Alfonso T García-Sosa; Ricardo L Mancera
Journal:  J Mol Model       Date:  2005-12-23       Impact factor: 1.810

8.  Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

Authors:  Jihyun Shim; Alexander D Mackerell
Journal:  Medchemcomm       Date:  2011-05       Impact factor: 3.597

9.  WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

Authors:  Alfonso T García-Sosa; Ricardo L Mancera; Philip M Dean
Journal:  J Mol Model       Date:  2003-05-17       Impact factor: 1.810

10.  Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames).

Authors:  Rafael M Couñago; Milya Davlieva; Ulrich Strych; Ryan E Hill; Kurt L Krause
Journal:  BMC Struct Biol       Date:  2009-08-20
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