LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking

被引：120

作者：

Velazquez-Libera, Jose Luis ^{[1
]}

Duran-Verdugo, Fabio ^{[1
]}

Valdes-Jimenez, Alejandro ^{[1
,2
]}

Nunez-Vivanco, Gabriel ^{[1
]}

Caballero, Julio ^{[1
]}

机构：

[1] Univ Talca, Ctr Bioinformat Simulat & Modelling, Talca 3460000, Chile

[2] Univ Politecn Cataluna, Comp Architecture Dept, Barcelona 08034, Spain

来源：

BIOINFORMATICS | 2020年 / 36卷 / 09期

关键词：

D O I：

10.1093/bioinformatics/btaa018

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

Motivation: Root mean square deviation (RMSD) is one of the most useful and straightforward features for structural comparison between different conformations of the same molecule. Commonly, protein-ligand docking programs have included some utilities that allow the calculation of this value; however, they only work efficiently when exists a complete atom label equivalence between the evaluated conformations. Results: We present LigRMSD, a free web-server for the automatic matching and RMSD calculations among identical or similar chemical compounds. This server allows the user to submit only a pair of identical or similar molecules or dataset of similar compounds to compare their three-dimensional conformations.

引用

页码：2912 / 2914

页数：3

共 10 条

[1]

GROMACS - A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION [J].

BERENDSEN, HJC ;

VANDERSPOEL, D ;

VANDRUNEN, R .

COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) :43-56

[2]

A maximum common substructure-based algorithm for searching and predicting drug-like compounds [J].

Cao, Yiqun ;

Jiang, Tao ;

Girke, Thomas .

BIOINFORMATICS, 2008, 24 (13) :I366-I374

[3]

RMSD and Symmetry [J].

Coutsias, Evangelos A. ;

Wester, Michael J. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2019, 40 (15) :1496-1508

[4]

Crystal structures of sampatrilat and sampatrilat-Asp in complex with human ACE - a molecular basis for domain selectivity [J].

Cozier, Gyles E. ;

Schwager, Sylva L. ;

Sharma, Rajni K. ;

Chibale, Kelly ;

Sturrock, Edward D. ;

Acharya, K. Ravi .

FEBS JOURNAL, 2018, 285 (08) :1477-1490

[5]

DeLano WL., 2002, The PyMOL Molecular Graphics System

[6]

pyRMSD: a Python']Python package for efficient pairwise RMSD matrix calculation and handling [J].

Gil, Victor A. ;

Guallar, Victor .

BIOINFORMATICS, 2013, 29 (18) :2363-2364

[7]

VMD: Visual molecular dynamics [J].

Humphrey, W ;

Dalke, A ;

Schulten, K .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1996, 14 (01) :33-38

[8]

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA [J].

Mena-Ulecia, Karel ;

Tiznado, William ;

Caballero, Julio .

PLOS ONE, 2015, 10 (11)

[9]

The Dynamic Nonprime Binding of Sampatrilat to the C-Domain of Angiotensin-Converting Enzyme [J].

Sharma, Rajni K. ;

Espinoza-Moraga, Marlene ;

Poblete, Horacio ;

Douglas, Ross G. ;

Sturrock, Edward D. ;

Caballero, Julio ;

Chibale, Kelly .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2016, 56 (12) :2486-2494

[10]

ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm [J].

Temelso, Berhane ;

Mabey, Joel M. ;

Kubota, Toshiro ;

Appiah-Padi, Nana ;

Shields, George C. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2017, 57 (05) :1045-1054

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