Software products provided for the scientific community

DrugScore, DrugScore^RNA, DrugScore^PPI, DrugScore²⁰¹⁸

• Scoring functions to predict protein-ligand, RNA-ligand, and protein-protein interactions
• A web server is available for DrugScore^PPI
• References: J. Mol. Biol. 2000, J. Chem. Inf. Model. 2007, Nucl. Acids Res. 2010, J. Chem. Inf. Model. 2019

AFMOC

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

RCNMA / NMSim

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

CNAnalysis

• 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 server is available for CNA
• References: Eng. Life Science 2008, Biophys. J. 2008, Proteins 2011, J. Chem. Inf. Model. 2013. 

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 

PocketAnalyzer^PCA

• 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

• End-point free energy calculations, structural decomposition of free energy, analysis of biomacromolecular dynamics
• References: J. Mol. Biol. 2003, J. Comput. Chem. 2004, J. Comput. Chem. 2005, J. Chem. Theory Comput. 2012

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

• Reference:   J. Chem. Inf. Model. 2019.

FEW_mem

• 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-S_vib

• Efficient approximation of vibrational entropy changes upon binding
• Reference: J. Chem. Theory Comput. 2017.

TopScore

• Highly accurate whole-protein and residue-wise model quality estimation using Deep Neural Networks
• Software download: TopScore download here.
• A web server is available for TopScore.
• Reference: J. Chem. Theory Comput. 2018.

TopModel

• Highly accurate template-based protein structure prediction using Deep Neural Networks
• Software download: TopModel download here.
• A web server is available for TopModel.
• Reference: J. Chem. Theory Comput. 2020.

TopDomain

• Protein domain boundary metaprediction combining multisource information and Deep Learning
• Software download: TopDomain download here.
• A web server is available for TopDomain.
• Reference: J. Chem. Theory Comput. 2021.

TopProperty

• Robust metaprediction of transmembrane and globular protein features using Deep Neural Networks
• Software download: TopProperty download here.
• A web server is available for TopProperty.
• Reference: J. Chem. Theory Comput. 2021.

Vasor

• MDR3 protein specific missense variant predictor.
• Software download: Vasor download here.
• A web server is available for Vasor.
• Reference: Hepatol. Commun. 2022.

TopEnzyme

• Database and framework for the coverage of functional (by enzyme commission) space for computationally generated enzyme structures.
• A web server is available for TopEnzyme.
• Reference: Bioinformatics 2023.

LISTER

• Semiautomatic metadata extraction from annotated experiment documentation in eLabFTW.
• The LISTER source code is available at GitHub.
• Reference: J. Chem. Inf. Model. 2023.