title: SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling.
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).
authors.affiliation: Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wang
authors.forename: Adrian A
authors.initials: AA
authors.lastname: Canutescu
authors.forename: Roland L
authors.initials: RL
authors.lastname: Dunbrack
mesh_terms: D000465:Algorithms; D008024:Ligands; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D008024:Ligands; D011506:Proteins