Software products provided for the scientific community

DrugScore, DrugScoreRNA, DrugScorePPI, DrugScore2018

AFMOC

RCNMA / NMSim

CNAnalysis

VisualCNA

  • 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 
PocketAnalyzerPCA
  • 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. 
MM-PBSA within the Amber suite of biomolecular simulation codes

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

FEWmem

  • 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.

BEERT

  • Efficient approximation of ligand rotational and translational entropy changes upon binding for use in MM-PBSA calculations
  • Reference: J. Chem. Inf. Model. 2017.

CNA-Svib

TopScore

  • 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.