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.
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:
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:
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.
Sequence analysis
A mathematica script to draw sequence logos: the code and auxiliary files are bundled into an archive.
Molecular evolution of proteins
We
are performing simulations of the neutral evolution of proteins and
protein-protein complexes. We employ lattice models and off-lattice
models to explore neutral networks of protein sequences, generated by
random point mutations and a simple selective pressure.
An
off-lattice simulation program is available.
Off-lattice simulation program. A beta version is available with documentation and examples.