Comparative Protein Structure Modeling Using Modeller

By Narayanan Eswar, Ben M. Webb, Marc A. Martí-Renom, Mallur Srivatsan Madhusudhan, David Eramian, Min-Yi Shen, Ursula Pieper, Andrej Sali. Current Protocols in Bioinformatics, 2006

2,348 citations recorded by the source corpus.

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three‐dimensional (3‐D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3‐D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3‐D 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 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.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/77d049b5961f57d9d42154144432a8fb039f1230

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Citations in the corpus

A position-specific distance-dependent statistical potential for protein structure and functional study (2012, methodology): “Then we used MODELER (Eswar et al., 2006) to build four different three-dimensional (3D) models for each target protein based upon the four alignments, respectively.”
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “MODELLER is used for homology or comparative modeling of protein three-dimensional structures (Eswar et al., 2001; Marti-Renom et al., 2000).”
Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, methodology): “These data, in combination with advances in homologymodeling (Chivian et al., 2003; Eswar et al., 2006; Zhang, 2007; Schwede et al., 2009) and MR programs, make MR an increasingly important approach to the phase problem in protein X-ray crystallography.”
A combined activation mechanism for the glucagon receptor (2020, methodology): “The fused T4 lysozyme was removed and mutations reverted to wild type using MODELLER (52).”