Comparative Protein Structure Modeling Using MODELLER

By Ben M. Webb, Andrej Sali. Current Protocols in Protein Science, 2016

548 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4e5bdfbe14fb8cf9a03c2c6ea60ea22942f11059

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In Materials Chemistry

1. Israel T. Desta
2. Kathryn A. Porter
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Citations in the corpus

• CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site (2015, unknown): “Final models are reconstructed from the C-alpha trace to an all-atom representation and subsequently undergo optimization using Modeller (17) with DOPE statistical potential (18).”
• What Method to Use for Protein-Protein Docking? (2019, methodology): “We attempted to identify templates for all these targets using HHPred [32] with default settings and built homology models of the dimers using MODELLER [33] from the templates found.”