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Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37. doi: 10.1002/cpbi.3.

Comparative Protein Structure Modeling Using MODELLER.

Author information

1
University of California at San Francisco, San Francisco, California.

Abstract

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.

KEYWORDS:

MODELLER; ModBase; comparative modeling; protein fold; protein structure; structure prediction

PMID:
27322406
PMCID:
PMC5031415
DOI:
10.1002/cpbi.3
[Indexed for MEDLINE]
Free PMC Article

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