Software products provided for the scientific community
DrugScore, DrugScoreRNA, DrugScorePPI, DrugScore2018
RCNMA / NMSim
MM-PBSA within the Amber suite of biomolecular simulation codes
- A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability
- Software available under GPL from here.
- Video tutorials are available on Youtube.
- References: Bioinformatics 2015
FEW within the Amber suite of biomolecular simulation codes
- Free energy workflow tool for binding free energy calculations with TI, MM-PBSA, and LIE for several ligands binding to the same receptor
- A tutorial demonstrating the functionality of FEW is available at http://ambermd.org/tutorials
- Reference: J. Comput. Chem. 2013.
PACKMOL-Memgen within the Amber suite of biomolecular simulation codes
- Implicit solvent / implicit membrane free energy calculations
- Extension of the free energy workflow FEW towards implicit solvent / implicit membrane MM-PBSA calculations
- Reference: Gen. Subjects 2015.
- Efficient approximation of ligand rotational and translational entropy changes upon binding for use in MM-PBSA calculations
- Reference: J. Chem. Inf. Model. 2017.