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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 :/