NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

被引：69

作者：

Gaudreault, Francis ^{[1
]}

Morency, Louis-Philippe ^{[1
]}

Najmanovich, Rafael J. ^{[1
]}

机构：

[1] Univ Sherbrooke, Fac Med & Hlth Sci, Dept Biochem, Sherbrooke, PQ J1K 2R1, Canada

来源：

BIOINFORMATICS | 2015年 / 31卷 / 23期

基金：

加拿大自然科学与工程研究理事会;

关键词：

LIGAND DOCKING; BINDING POCKETS; PROTEIN; IDENTIFICATION;

D O I：

10.1093/bioinformatics/btv458

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS.

引用

页码：3856 / 3858

页数：3

共 19 条

[1]

[Anonymous], PYMOL MOL GRAPHICS S

[2] Small-molecule ligand docking into comparative models with Rosetta [J].

Combs, Steven A. ;

DeLuca, Samuel L. ;

DeLuca, Stephanie H. ;

Lemmon, Gordon H. ;

Nannemann, David P. ;

Nguyen, Elizabeth D. ;

Willis, Jordan R. ;

Sheehan, Jonathan H. ;

Meiler, Jens .

NATURE PROTOCOLS, 2013, 8 (07) :1277-1298

[3] Analysis of Subpocket Selectivity and Identification of Potent Selective Inhibitors for Matriptase and Matriptase-2 [J].

Duchene, Dominic ;

Colombo, Eloic ;

Desilets, Antoine ;

Boudreault, Pierre-Luc ;

Leduc, Richard ;

Marsault, Eric ;

Najmanovich, Rafael .

JOURNAL OF MEDICINAL CHEMISTRY, 2014, 57 (23) :10198-10204

[4] FlexAID: Revisiting Docking on Non-Native-Complex Structures [J].

Gaudreault, Francis ;

Najmanovich, Rafael J. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2015, 55 (07) :1323-1336

[5] A method for localizing ligand binding pockets in protein structures [J].

Glaser, F ;

Morris, RJ ;

Najmanovich, RJ ;

Laskowski, RA ;

Thornton, JM .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 62 (02) :479-488

[6] SwissDock, a protein-small molecule docking web service based on EADock DSS [J].

Grosdidier, Aurelien ;

Zoete, Vincent ;

Michielin, Olivier .

NUCLEIC ACIDS RESEARCH, 2011, 39 :W270-W277

[7] Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions [J].

Huang, Sheng-You ;

Grinter, Sam Z. ;

Zou, Xiaoqin .

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2010, 12 (40) :12899-12908

[8] Automated Docking Screens: A Feasibility Study [J].

Irwin, John J. ;

Shoichet, Brian K. ;

Mysinger, Michael M. ;

Huang, Niti ;

Colizzi, Francesco ;

Wassam, Pascal ;

Cao, Yiqun .

JOURNAL OF MEDICINAL CHEMISTRY, 2009, 52 (18) :5712-5720

[9] Shape variation in protein binding pockets and their ligands [J].

Kahraman, Abdullah ;

Morris, Richard J. ;

Laskowski, Roman A. ;

Thornton, Janet M. .

JOURNAL OF MOLECULAR BIOLOGY, 2007, 368 (01) :283-301

[10]

Kramer B, 1999, MED CHEM RES, V9, P463

← 1 2 →