Article

SCWRL and MolIDE: Computer programs for side-chain conformation prediction and homology modeling

Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
Nature Protocol (Impact Factor: 8.36). 02/2008; 3(12):1832-47. DOI: 10.1038/nprot.2008.184
Source: PubMed

ABSTRACT SCWRL and MolIDE are software applications for prediction of protein structures. SCWRL is designed specifically for the task of prediction of side-chain conformations given a fixed backbone usually obtained from an experimental structure determined by X-ray crystallography or NMR. SCWRL is a command-line program that typically runs in a few seconds. MolIDE provides a graphical interface for basic comparative (homology) modeling using SCWRL and other programs. MolIDE takes an input target sequence and uses PSI-BLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target-template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side-chain conformations with SCWRL and a loop-modeling program for insertion-deletion regions with user-selected sequence segments. SCWRL and MolIDE can be obtained at (http://dunbrack.fccc.edu/Software.php).

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Available from: Roland Dunbrack, Sep 01, 2015
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