GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

被引：55

作者：

Esguerra, Mauricio ^{[1
]}

Siretskiy, Alexey ^{[1
]}

Bello, Xabier ^{[2
]}

Sallander, Jessica ^{[1
]}

Gutierrez-de-Teran, Hugo ^{[1
]}

机构：

[1] Uppsala Univ, Biomed Ctr, Dept Cell & Mol Biol, Box 596, SE-75124 Uppsala, Sweden

[2] Hosp Clin Univ Santiago, Fdn Publ Galega Med Xenom, Santiago De Compostela 15706, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / W1期

关键词：

STRUCTURE VALIDATION; SEQUENCE ALIGNMENT; PREDICTIONS; INSIGHTS;

D O I：

10.1093/nar/gkw403

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：

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.

引用

页码：W455 / W462

页数：8

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