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A general screened Coulomb potential based implicit solvent model: Calculation of secondary structure of small peptides (https://doi.org/10.1002/qua.1210)
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MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein–Protein Docking (https://doi.org/10.1021/ct300497z)
Rev 5 - February 2021
- Fixed bugs in PDB atom typing and protein typing based on dictionary
- Fixed bugs in PDB procesing (multichain systems)
- Automatic charges for protein (AMBER) and ligand (PEOE) in PDBs
- Unitary tests
Rev 4 - March 2018
- Added full vdW/qq/solv residue decomposition in output for COMBINE-like methods
- Added support for XTC GROMACS trajectories (still require AMBER topology)
- Excluded atoms mask selects individual atoms and not full residues to allow
better analysis of protein interfaces and Ala-scanning
- LAPACK can be disabled on copilation time to enable a more portable code
Rev 3 - January 2016
- MultiPDB support (experimental) for GROMACS exports
Rev 2 - November 2015
- Finished QH entropy approximation. Fixed bugs.
- Multiple files trajectories (experimental, limited naming scheme)
- Exclusion regions for protein regions analysis
- Fixed bugs regarding residue decomposition
Rev 1 - January-April 2014
C reimplementation with fancy stuff:
- No dry topology needed. Waters/ions stripped on-the-fly
- "Advanced" atom masks to select ligand
- Automatic "box info" detection
- PDB with residue contributions in b-factor columns
- Much better memory management (no more SegFaults on < 2Gb boxes).
But OVERLAPS still limited to 300
- Corrected Hydrogen bond model (no more ionic problems). 3 layers
- Simpler output (parseable CSV files)
- Debug info control
- Quasiharmonic entropy approximation thanks to the indexation of
the trajectory
- Faster/Slower depending on the case than Fortran MMISMSA :/