Software products provided for the scientific community
DrugScore, DrugScoreRNA, DrugScorePPI, DrugScore2018
RCNMA / NMSim
- A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability
- Software is available under GPL here.
- Video tutorials are available on Youtube.
- References: Bioinformatics 2015
MM-PBSA within the Amber suite of biomolecular simulation codes
- Generation of pocket-space maps to identify novel binding-site conformations in proteins
- Software available under an open-source license here.
- Reference: J. Chem. Inf. Model. 2011.
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 the Amber Tutorial.
- 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.
- Highly accurate whole-protein and residue-wise model quality estimation using Deep Neural Networks
- After downloading the different parts of the TopScore tar-ball, combine the parts using: cat standalone_topscore.tar.gz.parta* > standalone_topscore.tar.gz
- Software download: TopScore download here.
- Data set: TopScore data set download here.
- Reference: J. Chem. Theory Comput. 2019.