MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

被引：116

作者：

Meyer, Tim ^{[1
,2
]}

D'Abramo, Marco ^{[1
]}

Hospital, Adam ^{[1
,3
]}

Rueda, Manuel ^{[1
]}

Ferrer-Costa, Carles ^{[1
]}

Perez, Alberto ^{[1
,2
]}

Carrillo, Oliver ^{[1
]}

Camps, Jordi ^{[1
,2
,3
]}

Fenollosa, Caries ^{[1
,3
]}

Repchevsky, Dmitry ^{[1
,2
,3
]}

Lluis Gelpi, Josep ^{[1
,2
,3
,4
]}

Orozco, Modesto ^{[1
,2
,3
,4
]}

机构：

[1] Inst Res Biomed, Joint IRB BSC Computat Biol Programme, Barcelona 08028, Spain

[2] Barcelona Supercomp Ctr, Barcelona 08034, Spain

[3] Natl Inst Bioinformat, Barcelona 08028, Spain

[4] Univ Barcelona, Fac Biol, Dept Bioquim & Biol Mol, E-08028 Barcelona, Spain

来源：

STRUCTURE | 2010年 / 18卷 / 11期

关键词：

FORCE-FIELD; SIMULATION; PROTEINS; TOOL; DYNAMEOMICS; SEQUENCES; EFFICIENT;

D O I：

10.1016/j.str.2010.07.013

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. The trajectories and analyses are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. Here, we describe the project and the structure and contents of our database, and provide examples of how it can be used to describe the global flexibility properties of proteins. Basic analyses and trajectories stripped of solvent molecules at a reduced resolution level are available from our web server.

引用

页码：1399 / 1409

页数：11

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