title: Comparative protein structure modeling using Modeller.
abstract: 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.
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: Narayanan
authors.initials: N
authors.lastname: Eswar
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: Ben
authors.initials: B
authors.lastname: Webb
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: M S
authors.initials: MS
authors.lastname: Madhusudhan
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: David
authors.initials: D
authors.lastname: Eramian
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: Min-Yi
authors.initials: MY
authors.lastname: Shen
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.affiliation: University of California at San Francisco San Francisco, California.
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins