Literature DB >> 12142469

Protein flexibility and computer-aided drug design.

Chung F Wong1, J Andrew McCammon.   

Abstract

Although computational techniques are increasingly being used in computer-aided drug design, the effects due to protein flexibility are still ignored in many applications. This review revisits rigorous statistical mechanical methods for predicting binding affinity, discusses some recent developments for improving their speed and reliability, and examines faster approximate models for facilitating virtual screening and lead optimization.

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Year:  2002        PMID: 12142469     DOI: 10.1146/annurev.pharmtox.43.100901.140216

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


  19 in total

1.  Stabilization of anionic and neutral forms of a fluorophoric ligand at the active site of human carbonic anhydrase I.

Authors:  Sumathra Manokaran; Jayati Banerjee; Sanku Mallik; D K Srivastava
Journal:  Biochim Biophys Acta       Date:  2010-07-08

Review 2.  Protein dynamics via computational microscope.

Authors:  Anton B Guliaev; Senping Cheng; Bo Hang
Journal:  World J Methodol       Date:  2012-12-26

3.  Using machine learning to improve ensemble docking for drug discovery.

Authors:  Tanay Chandak; John P Mayginnes; Howard Mayes; Chung F Wong
Journal:  Proteins       Date:  2020-05-25

Review 4.  Computational systems chemical biology.

Authors:  Tudor I Oprea; Elebeoba E May; Andrei Leitão; Alexander Tropsha
Journal:  Methods Mol Biol       Date:  2011

5.  Role of dynamics in the autoinhibition and activation of the exchange protein directly activated by cyclic AMP (EPAC).

Authors:  Bryan VanSchouwen; Rajeevan Selvaratnam; Federico Fogolari; Giuseppe Melacini
Journal:  J Biol Chem       Date:  2011-08-26       Impact factor: 5.157

6.  A flexible docking scheme to explore the binding selectivity of PDZ domains.

Authors:  Z Nevin Gerek; S Banu Ozkan
Journal:  Protein Sci       Date:  2010-05       Impact factor: 6.725

7.  The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers.

Authors:  Zhong Zheng; P Leslie Dutton; M R Gunner
Journal:  Proteins       Date:  2010-09

8.  Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites.

Authors:  Narender Singh; James M Briggs
Journal:  Biopolymers       Date:  2008-12       Impact factor: 2.505

9.  Development of a new predictive model for interactions with human cytochrome P450 2A6 using pharmacophore ensemble/support vector machine (PhE/SVM) approach.

Authors:  Max K Leong; Yen-Ming Chen; Hong-Bin Chen; Po-Hong Chen
Journal:  Pharm Res       Date:  2008-12-23       Impact factor: 4.200

10.  Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein.

Authors:  Ami Y-C Yang; Ricardo L Mancera
Journal:  J Comput Aided Mol Des       Date:  2008-04-15       Impact factor: 3.686

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