The Program MolDyn
is designed to perform multiple tasks with protein structure:
- 1) restoration of missing coordinates of heavy atoms of side chains;
- 2) restoration of missing coordinates of all hydrogen atoms;
- 3) optimization of a protein structure via local energy optimization in an implicit/explicit water solvent;
- 4) optimization of a protein structure via MD simulation in water solvent;
- 5) optimization and folding of a protein via a user defined simulated annealing protocol
coupled with force field variation;
- 6) optimization of a user defined flexible protein segments with user defined restraints;
- 7) simulation of the molecular dynamical trajectory for molecular atomic coordinates and potential
energy for statistical analysis;
- 8) exhaustive docking of flexible ligand molecule of size up to ~ 100 atoms to protein molecule.
MolDyn description
MolDyn parameters
MolDyn parameter and Input file description
Test examples description
Docking of Ligand on Protein
