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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.
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SCWRL Availability
Speed
Accuracy
Installation
Usage
Contact
SCWRL3.0 is the most recent version of the SCWRL program for prediction of protein
side-chain conformations. SCWRL3.0 is based on an algorithm based
on graph theory that solves the combinatorial problem in side-chain
prediction more rapidly than many other available program. SCWRL3.0 is
more accurate than previous versions of SCWRL, while the graph theory
algorithm will allow for development of more sophisticated energy
functions and for incorporation of side-chain flexibility around
rotameric positions.
The SCWRL3 paper
has been published by Protein Science. A reprint is available.
Please cite the paper: A. A. Canutescu, A. A. Shelenkov, and R. L. Dunbrack, Jr. A graph theory algorithm for protein side-chain prediction. Protein Science 12, 2001-2014 (2003).
Availability:
SCWRL3.0 is free to researchers in non-profit institutions. Obtaining SCWRL3.0 is fast and easy. The 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, 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 SCWRL3.0.
Speed:
SCWRL3.0 is much faster than previous versions of SCWRL. Previous versions of
SCWRL used two parameters to reduce the complexity of the search
problem among clusters of interacting side chains. These are EBBMIN
and EPAIRMIN. EBBMAX is the maximum backbone/sidechain interaction
energy for a rotamer to be included in the calculations. EPAIRMIN is
the minimum side-chain/side-chain interaction energy for two residues
to be considered connected in determining clusters of interacting
residues that must be resolved to find the global minimum energy.
Raising EBBMAX increases the size of the calculation by increasing
the number of rotamers for each side chain. Decreasing EPAIRMIN
increases the size of the calculation by increasing the number of
neighboring side chains interacting with each rotamer of a side
chain. In the table below, we show the time required to predict the
side-chain conformations in 180 proteins comprising 34,342 side
chains. We capped the time spent on any one protein to 15 minutes
maximum. The times given include only those proteins that could be
solved in 15 minutes or less. The parameter defaults for SCWRL2.95
(the last publicly released version of SCWRL) and SCWRL3.0 are marked
by "*".
| | SCWRL2.95 | SCWRL3.0 |
| EBBMIN | EPAIRMIN | Time(sec) |
N Completed | Time(sec) | N Completed |
| 5 | 10 | * 1012 | 180 | 234 | 180 |
| 5 | 0 | 3430 | 174 | 228 | 180 |
| 50 | 10 | 8549 | 168 | 395 | 180 |
| 50 | 0 | 15537 | 132 | * 404 | 180 |
| 8 | 0 | N.D. | N.D. | 790 | 180 |
N.D. Not done.
Accuracy:
SCWRL3.0 is more accurate than SCWRL2.95. The table
below gives the accuracy in chi1 and chi1+2 dihedral angles for a
test set of 180 proteins.χ1
prediction accuracy is expressed as percent of side chains with χ1
dihedral angles within 40° of the X-ray crystallographic value.
For side chains with only χ1,
the χ1 accuracy is given in
the χ1+2 columns. 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 SCWRL3.0 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").
| |
χ1 Prediction Accuracy |
χ1+2 Prediction Accuracy |
| Residue Type | Num. of Residues |
BBDep | SCWRL2.95 | SCWRL3.0 |
BBDep | SCWRL2.95 | SCWRL3.0 |
| PHE | 1653 | 75.4 | 92.9 | 93.7 | 68.3 | 84.9 | 87.4 |
| TYR | 1633 | 74.1 | 91.0 | 92.3 | 68.9 | 83.8 | 86.5 |
| ILE | 2134 | 87.7 | 91.8 | 91.8 | 70.1 | 78.1 | 80.4 |
| LEU | 3406 | 72.9 | 89.0 | 89.9 | 66.1 | 80.1 | 81.8 |
| VAL | 2787 | 85.9 | 89.3 | 89.9 | 85.9 | 89.3 | 89.9 |
| TRP | 671 | 68.4 | 87.0 | 88.4 | 41.3 | 60.6 | 64.8 |
| CYS | 679 | 80.6 | 86.5 | 88.2 | 80.6 | 86.5 | 88.2 |
| THR | 2449 | 85.0 | 87.4 | 88.0 | 85.0 | 87.4 | 88.0 |
| HIS | 899 | 67.7 | 83.3 | 85.3 | 59.3 | 66.4 | 75.1 |
| PRO | 1994 | 82.6 | 83.9 | 84.4 | 82.6 | 83.9 | 84.4 |
| ASP | 2493 | 71.7 | 80.2 | 80.8 | 62.6 | 56.5 | 70.4 |
| MET | 789 | 64.9 | 76.9 | 80.4 | 37.8 | 59.8 | 65.1 |
| ASN | 2036 | 68.1 | 77.9 | 78.7 | 55.6 | 56.9 | 66.1 |
| ARG | 1888 | 62.6 | 75.8 | 76.9 | 48.7 | 61.9 | 63.7 |
| GLN | 1569 | 66.1 | 74.0 | 74.6 | 40.9 | 54.7 | 52.6 |
| LYS | 2319 | 66.5 | 73.9 | 74.0 | 46.8 | 57.0 | 57.0 |
| GLU | 2267 | 61.7 | 70.0 | 71.3 | 39.9 | 50.5 | 51.7 |
| SER | 2676 | 62.6 | 65.7 | 66.4 | 62.6 | 65.7 | 66.4 |
| ALL | 34342 | 73.0 | 81.7 | 82.6 | 63.2 | 70.9 | 73.7 |
Installation:
SCWRL3.0 is provided in binary form for the following operating systems:
- Windows 9x/Me/2000/XP
- Linux
- MacOS X
- SGI Irix
- SunOS
and the installation kits for each operating system have the following names, respectively:
- scwrl3_win.zip
- scwrl3_lin.tar.gz
- scwrl3_mac.tar.gz
- scwrl3_sgi.tar.gz
- scwrl3_sun.tar.gz
After you download the installation kit appropriate for your operating system, you should create a directory and uncompress it:
- for Windows, you have to use WinZip
- for Linux / MacOS X /SGI Irix / SunOS, you have to ungzip and untar the
appropriate installation kit. For example, for Linux:
- gzip -d scwrl3_lin.tar.gz
- tar -xf scwrl3_lin.tar
The previous step will generate 4 files:
- BBDep.bin
- setup (setup.exe for Windows)
- scwrl3_
- README.scwrl3
The final installation step is to run setup (setup.exe for Windows) from the directory in which you uncompressed the kit.
Simply type:
./setup
to the Linux shell or MacOS X or SGI Irix or SunOS terminal window, or
setup.exe
to the command window for Windows.
Running setup will generate an executable file scwrl3 (scwrl3.exe for Windows) and will also hardcode the path toward the backbone-dependent rotamer library (BBDep.bin). After this, you can move the scwrl3 executable to a different location, or create symbolic links or aliases for it, provided that you keep the backbone-dependent rotamer library in the directory you performed the installation. If you decide to move the backbone-dependent rotamer library in a different location, you have to repeat the installation procedure for that directory, beginning with uncompressing the kit.
Usage:
scwrl −i inputpdbfile −o outputpdbfile [−s sequencefile −f framefile −u −d] > logfile
Optional flags:
-u disables the disulfide bonds identification
-s loads a sequence file
-f loads a frame file
-d prints dihedral angles to a file called outputpdbfile.dihed
-i [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 [required]
The output file contains the identical backbone as the input file,
with predicted coordinates for the sidechains.
-f [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 [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.
-u [optional]
Disulfides will not be calculated
-d [optional]
Specifies dihedral angles to be printed in a file with the same name
as the output pdb file with the extension .dihed added
Contact the authors
Adrian Canutescu
Roland Dunbrack
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