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

Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
Nature Protocol (Impact Factor: 9.67). 02/2008; 3(12):1832-47. DOI: 10.1038/nprot.2008.184
Source: PubMed


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 (

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Available from: Roland Dunbrack, Oct 04, 2015
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    • "The most reliable models were evaluated on the basis of root mean square deviation (RMSD), TM score and DOPE Profile. The selected models were further refined using SCWRL 4.0 (Wang et al., 2008) and CHARMm (Vanommeslaeghe et al., 2010) energy minimization using ChiRotor algorithm of DS. The GROMOS (van Gunsteren et al., 1996) algorithm implemented in DeepView (Kaplan and Littlejohn, 2001) was used for energy minimization of the predicted chitinase II structure. "
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    Journal of Theoretical Biology 04/2015; 374. DOI:10.1016/j.jtbi.2015.03.035 · 2.12 Impact Factor
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    • "The XML files from the SIFTS database (Velankar et al., 2005) were used to find the residue correspondence between the UniProt and PDB sequences. For each unique PDB sequence, we used one iteration of our modified PSI-BLAST (Altschul et al., 1997) from MolIDE (Wang et al., 2008) to generate a profile from sequences in the UniRef90 database (Li et al., 2000). The parameters for PSI-BLAST were '-e 10 -h 0.0001 -v 5000 -b 5000 -N 25 -f 16'. "
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    Bioinformatics 08/2012; 28(21):2763-72. DOI:10.1093/bioinformatics/bts533 · 4.98 Impact Factor
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    • "Only residues in the PDB file which have a relative solvent accessibility, calculated by DSSP (Kabsch and Sander, 1983), above 40% are allowed to be mutated. This restriction was chosen because mutating buried residues may lead to unfolding (Wang, et al., 2008). The server can analyze the effect of a particular mutation of interest with a very good accuracy, compared to more approximate methods (Fogolari, et al., 2012). "
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