SCWRL

Bower, Cohen, SCWRL Backbone-dependent Log( rotamer prob) +... 

Mean-field approximation 20 self-bb proteins 87.7% xu 85.7% X12, core better than SCWRL, surface not... 

SCWRL uses an alternative strategy, based on a probabilistic potential based on the backbone-dependent rotamer library. There are two terms the internal side-chain energy and the local side-chain-backbone interaction are modeled with an energy term proportional to —In prot where prot is the probability of the rotamer for the particular side-chain type and backbone conformation and a simple truncated linear steric term that models the repulsive interactions between atoms [93, 94]. 

Residue Number BBIND BBDEP CONFMAT RAMP SCWRL SIDEMOD SMD TORSO... 

SCWRL X http //www.fccc.edu/research/labs/ dunbrack/ scwrl... 

R. L. Dunbrack, Jr. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Proteins Suppl. 1999, Suppl. 3, 81-87. 

Wang, Q., Canutescu, A.A., and Dunbrack, R.L. (2008) SCWRL and MolIDE computer programs for side-chain conformation prediction and homology modeling. Nature Protocols, 3, 1832-1847. 

SCWRL Fox Chase Cancer Center dunbrack.fccc.edu/scwrl4 15... 

The SCWRL program for placing sidechains is able to reproduce crystal structure sidechains to about 2 A RMSD. In early (unpublished) work, we used average side chain rotamers, not dependent on backbone torsion angles, and the resulting scores were much lower than the SCWRL scores. In fact, the template backbones with SCWRL-placed sidechains score as well as template backbones with sidechains taken from the known crystal structure of the query sequence. 

Side-Chains with Rotamer Library (SCWRL)... 

The rotamer library used by SCWRL is backbone-dependent. Such libraries are considered to be more accurate than a backbone-independent rotamer library. A backbone-dependent rotamer library is more robust because the side-chain conformations are based on the protein s backbone dihedral angles ( and Both the secondary structure and the... 

Graph-Theory Algorithm for Rapid Protein Side-Chain Prediction. Download SCWRL from http //dunbrack.fccc.edu/SCWRL3.php. 

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