Comparative Protein Structure Modeling Using MODELLER | Zendy

Webb Benjamin | Zendy; Sali Andrej | Zendy

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Comparative Protein Structure Modeling Using MODELLER

Author(s) -

Webb Benjamin,

Sali Andrej

Publication year - 2016

Publication title -

current protocols in protein science

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.409

H-Index - 32

eISSN - 1934-3663

pISSN - 1934-3655

DOI - 10.1002/cpps.20

Subject(s) - modeller , computer science , casp , protein structure prediction , template , protein structure , computational biology , homology modeling , programming language , chemistry , biology , biochemistry , enzyme

Comparative protein structure modeling predicts the three‐dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.

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