Available software and data

Protein-protein complexes: a large decoy library

• Native and decoy structures.

Protein sequences obtained by computational design

• Native and designed sequences.

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.

• Generalized Born code for XPLOR 3.8

• Generalized Born code for CNS

• 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.