Comparative protein structure modeling using MODELLER.
Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an 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.
Eswar
Narayanan
N
University of California at San Francisco, San Francisco, California, USA.
Webb
Ben
B
Marti-Renom
Marc A
MA
Madhusudhan
M S
MS
Eramian
David
D
Shen
Min-Yi
MY
Pieper
Ursula
U
Sali
Andrej
A
D000818:Animals; D020407:Internet; D007770:L-Lactate Dehydrogenase / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D014246:Trichomonas vaginalis / Q000201:enzymology
D007770:L-Lactate Dehydrogenase