Protein Structural Statistics with PSS
PSS is a protein structural statistics program for Unix-like environments. It is written in Perl, has a command-line interface, and is distributed under the GNU General Public License.
T. Gaillard, B.B.L. Schwarz, Y. Chebaro, R.H. Stote, A. Dejaegere
J. Chem. Inf. Model. 2013, 53, 2471-2482.
Force field for tetracyclines, compatible with the
Charmm27 protein force field
(see Aleksandrov & Simonson, Journal of Computational Chemistry, 2009, 30:243-255 and 2006, 27:1517-1533)
We have developed a molecular mechanics force field for several tetracycline variants, in different protonation states, which is consistent with the Charmm27 force field for proteins and nucleic acids.
The force field files are available including documentation and examples.
Force field for imatinib (Gleevec), compatible
with the Charmm27 protein force field
(see Aleksandrov & Simonson, Journal of Computational Chemistry, 2010, 31:1550-60
We have developed a molecular mechanics force field for several imatinib variants, in their main protonation state, which is consistent with the Charmm27 force field for proteins and nucleic acids:
AMBER to XPLOR force field conversion (by Thomas Gaillard)
This is a conversion of AMBER force fields to XPLOR format. Force fields included are:
toppar_ff94.str corresponds to leaprc.ff94 (Cornell topologies with parm94)
toppar_ff99.str corresponds to leaprc.ff99 (Cornell topologies with parm99)
toppar_ff99SB.str corresponds to leaprc.ff99SB (Cornell topologies with parm99 + frcmod.ff99SB)
toppar_ff99bsc0.str corresponds to leaprc.ff99bsc0 (Cornell topologies with parm99 + frcmod.ff99SB + frcmod.parmbsc0)
Topology and parameter files as well as documentation and examples are available. The archive contains the topology and parameter files for XPLOR as well as a README file explaining the technical details and reliability of the conversion, and examples of peptide and nucleic acid building.
Protein-protein complexes: a large decoy library (Launay and Simonson, J Comp Chem 2011, 32:106-120)
We have produced a large set of decoy structures using a flexible docking procedure: about 300,000 decoys for 243 different complexes, or 1200 decoys per complex. The structures, their physical-chemical characterization, and more information are available at the link below:
Biomolecular simulation and structure refinement
Generalized Born code: see L Moulinier, D Case & T Simonson (2004) Acta Cryst D59, 2094-2103;
Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.
DialX: Torsion angle plotting program for use with XPLOR, NIH-XPLOR, CNS or CHARMM trajectories.
Protein sequences obtained by computational protein design (Schmidt am Busch et al, Proteins 2009 and Plos One 2010)
Sequences were produced by computational protein design for about 90 proteins, taken from six SCOP families. The best sequences are available at the link below:
by Thomas Simonson. Last modified, 11/08/13.