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% of chi1 angles and 75% of chi1+2 are predicted correctly within 40 degrees of the X-ray positions. Among side chains with higher electron density (25th-100th percentile), these numbers rise to 89% and 80%. The new program maintains its simple command-line interface, designed for homology modeling. To achieve higher accuracy, SCWRL4 is somewhat slower than SCWRL3 when run in the default flexible rotamer model (FRM) by a factor of 3-6, depending on the protein. When run in the rigid rotamer model (RRM), SCWRL4 is about the same speed as SCWRL3. In both cases, SCWRL4 will converge on very large proteins or protein complexes or those with very dense interaction graphs, while SCWRL3 sometimes would not.
SCWRL4.0 is free to researchers in non-profit institutions. Obtaining SCWRL4.0 is fast and easy.
The non-profit/academic license form is available here. Just click and then fill out the form and click "I agree". You will get a page with your submitted data for you to check. Then make sure you hit "Send request" to complete the license request. Note: if you submit a blank request or nonsense information, you will not get a response from us.
Individuals in for-profit institutions should contact Roland Dunbrack to obtain information on a commercial license for SCWRL4.0.
Installers for SCWRL4 are provided for the following operating systems:
scwrl4 −i inputpdbfilename −o outputpdbfilename > logfilenameRequired flags:
Improved prediction of protein side-chain conformations with SCWRL4.
G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr., Proteins: Structure, Function, Bioinformatics 2009, 77(4): 778-795. Article
SCWRL4.0 is more accurate than SCWRL3. The table below gives the accuracy in χ1 and χ1+2 dihedral angles for a test set of 379 proteins. Accuracy is given for those side chains with electron density from the 25th-100th percentiles (see Shapovalov and Dunbrack, Proteins, 66:279-303 (2007)). χ1 prediction accuracy is expressed as percent of side chains with χ1 dihedral angles within 40° of the X-ray crystallographic value. For χ1+2 to be correct, both χ1 and χ2 must be within 40° of their X-ray values. Residue types are sorted by their SCWRL4.0 χ1 accuracy. For comparison, the accuracy of choosing rotamers just based on the rotamer with maximum probability from the backbone-dependent rotamer library is also given ("BBDEP").
|Residue Type||Num. of Residues||BBDep||SCWRL3||SCWRL4.0||BBDep||SCWRL3||SCWRL4.0|