MolIDE: You may be interested in our graphical user interface for homology modeling with SCWRL that includes
PSI-BLAST searches of the PDB, PSIPRED secondary structure predictions, structurally assisted alignment editing,
and loop and side-chain modeling. You need to obtain the two programs with separate licenses.
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.
The SCWRL4 paper has been published in Proteins: Structure, Function, Bioinformatics. A reprint is available.
Please cite the paper: G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009).
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.
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").
Installers for SCWRL4.0 are provided for the following operating systems:
Macintosh OS X (Intel)
and the installation kits for each operating system have the following names, respectively:
The Windows version is an installer. Just double-click on it and follow the directions. By default it will place the program in C:\FCCC\scwrl4_win. This is also where MolIDE expects to find SCWRL. Installation is complete. For the Linux and Macintosh OS X versions, simply exeucute the file on the command line and follow the instructions. The program will ask for a location to install the program in. Once installed, the program will expect to find the rotamer library in the installation directory. In order to move the rotamer library, reinstall the software.
-i <inputfilename> Input file in PDB format of required N,CA,C,O atoms
-o <outputfilename> Output file in PDB format including predicted side-chain coordinates
-f <framefilename> Input file in PDB format of ligand coordinates (see below for format)
-s <sequencefilename> Sequence file for specifying new sequence of fixed side chains
-p <paramfilename> Input file of parameters
-h Disable output of hydrogen atoms
-t Disable capping of N and C terminal residues with HN and OXT atoms
-# Calculate side-chain conformations of crystal
-i <inputfilename> [required] The main input file to scwrl should be a protein backbone, with or
without sidechains, cofactors, or solvent. Residues with incomplete
backbones are treated as glycines. Residues with names that do not
match the standard 20 amino acid names are also treated as
glycines. The sequence of residues is read from the first atom in each
residue. If you wish to change this sequence, the -s flag allows you
to enter a new sequence independently.
-o <outputfilename> [required] The output file contains the identical backbone as the input file,
with predicted coordinates for the sidechains.
-f <framefilename> [optional] This file is used to add additional steric boundaries to the
sidechains. It should be in pdb format, and might contain cofactors or
metal atoms, lipid molecules, or another protein. In any case, it is
held fixed and used only for steric clash checks.Radii were determined
from atom-atom distances in the PDB. All elements currently observed
in the PDB can be treated by scwrl.
-s <sequencefilename> [optional] This flag is followed by a sequence file. The sequence should have
the same number of residues in it as the input backbone. White space,
carriage returns, and numbers are ignored. Lower-case letters in the
sequence indicate that the Cartesian coordinates for the corresponding
residues are to be left untouched, and will be treated as steric
boundaries only for the other side chains.
Examples: SDERYCNM - full SCWRL side-chain replacement
SdERYCNM - input residue (aspartate) is left where as is.
SxERYCNM - input residue (aspartate) is left where as is.
-p <paramfilename> [optional] File that specifies parameters for SCWRL4. The default file is set during installation; if it is not present in that location, SCWRL4 will look in the current directory and in the directory where the executable is located. These options can be overridden using this flag.
-# [optional] Perform calculation of side-chain conformations within the crystal. Requires CRYST1 record in inputfilename. SCWRL4 uses crystal symmetry to build backbone and side-chain coordinates of asymmetric units neighboring the input coordinates.
-h [optional] Disables the output of hydrogen atom coordinates.
-t [optional] Disables adding hydrogens to the N-terminal nitrogen atom. By default, only a residue numbered 1 will be treated as N-terminal. Disables addition of OXT atom to C-terminal residue for each chain.