Current Protocols in Protein Science · 2016 · 761 citations · 202 references
Life SciencesBioinformaticsBiologyComputational BiologyStructural BioinformaticsStructural BiologyComparative ModelingHomology ModelingProtein Sequence AnalysisProtein StructureProtein Structure ModelingTemplate-based ModelingFold AssignmentFold MappingModel Performance EvaluationPredictionProtein Structure ComparisonTarget-template AlignmentTemplate-based Model EvaluationTemplate-based Protein Structure Prediction
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. © 2016 by John Wiley & Sons, Inc.
202
Julie Thompson, Desmond G. Higgins, Toby J. Gibson · Nucleic Acids Research · 1994 · 64.9K citations · Full text
MUSCLE: multiple sequence alignment with high accuracy and high throughput
R. C. Edgar · Nucleic Acids Research · 2004 · 46.5K citations · Full text
Helen M. Berman · Nucleic Acids Research · 2000 · 39.8K citations