Software products provided for the scientific community
- Structure-based 3D QSAR method for lead optimization
RCNMA / NMSim
- Multi-scale methods for modeling macromolecular conformational transitions
- A web service is available for RCNMA/NMSim
- Rigidity theory-based analysis of structural stability and flexibility of proteins and RNA
- Software available under an academic license, please contact Prof. Holger Gohlke
- A web service is available for CNA
- 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: Submitted 2014.
MM-PBSA within the Amber suite of biomolecular simulation codes
- End-point free energy calculations, structural decomposition of free energy, analysis of biomacromolecular dynamics
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
- Case study on ligand binding to FXa according to the below study published in J. Comput. Chem. 2013