swMATH ID: 22393
Software Authors: G. G. Krivov, M. V. Shapovalov, R. L. Dunbrack, Jr.
Description: Improved prediction of protein side-chain conformations with SCWRL4. SCWRL4 is based on a new algorithm and new potential function that results in improved accuracy at reasonable speed. This has been achieved through: 1) a new backbone-dependent rotamer library based on kernel density estimates; 2) averaging over samples of conformations about the positions in the rotamer library; 3) a fast anisotropic hydrogen bonding function; 4) a short-range, soft van der Waals atom-atom interaction potential; 5) fast collision detection using k-discrete oriented polytopes; 6) a tree decomposition algorithm to solve the combinatorial problem; and 7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group. Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low electron density and presumed conformational disorder. For a testing set of 379 proteins, 86
Homepage: http://dunbrack.fccc.edu/scwrl4/
Related Software: CHARMM; I-TASSER; iDNA-Methyl; 3DIGARS; iNitro-Tyr; iCTX-Type; iRSpot-PseDNC; iPPI-Esml; iPro54-PseKNC; PredLactamase; BULL!; BetaSCP2; CPLEX; QTFier; RASP; BetaSCP; Miniball; PAPI; MODELLER; CUDA
Cited in: 6 Publications

Citations by Year