Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics-Reference-Cited by-同舟云学术

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Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Published:2013-12 Issue:12 Volume:27 Page:989-1007
ISSN:0920-654X
Container-title:Journal of Computer-Aided Molecular Design
language:en
Short-container-title:J Comput Aided Mol Des

Author:

Wang Kai,Chodera John D.,Yang Yanzhi,Shirts Michael R.

Publisher

Springer Science and Business Media LLC

Subject

Physical and Theoretical Chemistry,Computer Science Applications,Drug Discovery

Link

http://link.springer.com/content/pdf/10.1007/s10822-013-9689-8.pdf

Reference70 articles.

1. Schneider G (2010) Virtual screening: an endless staircase? Nat Rev Drug Discov 9(4):273–276

2. B-Rao C, Subramanian J, Sharma SD (2009) Managing protein flexibility in docking and its applications. Drug Discov Today 14(7–8):394–400

3. Lie MA, Thomsen R, Pedersen CNS, Schiøtt B, Christensen MH (2011) Molecular docking with ligand attached water molecules. J Chem Inf Model 51(4):909–917

4. Thompson DC, Humblet C, Joseph-McCarthy D (2008) Investigation of MM-PBSA rescoring of docking poses. J Chem Inf Model 48(5):1081–1091

5. Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK (2008) Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol 377(3):914–934

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