Software products provided for the scientific community

• Scoring functions to predict protein-ligand, RNA-ligand, and protein-protein interactions
  
• A web service is available for DrugScore^PPI
  
• References: J. Mol. Biol. 2000, J. Chem. Inf. Model. 2007, Nucl. Acids Res. 2010.

• Structure-based 3D QSAR method for lead optimization
• References: J. Med. Chem. 2002, J. Med. Chem. 2005, J. Chem. Inf. Model. 2007.

• Multi-scale methods for modeling macromolecular conformational transitions
• A web service is available for RCNMA/NMSim
• Reference: Proteins 2006, Biophys. J. 2006, J. Chem. Inf. Model. 2011, Nucl. Acids Res. 2012.
  

• 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
• References: Eng. Life Science 2008, Biophys. J. 2008, Proteins 2011, J. Chem. Inf. Model. 2013.
  

• Generation of pocket-space maps to identify novel binding-site conformations in proteins
• Software available under an open-source license (http://sourceforge.net/projects/papca/)
  
• Reference: J. Chem. Inf. Model. 2011.

• End-point free energy calculations, structural decomposition of free energy, analysis of biomacromolecular dynamics
• References: J. Mol. Biol. 2003, J. Comp. Chem. 2004, J. Comp. Chem. 2005.