Dr. Daria Kokh

Research interests

• Machine Learning methods in drug design: prediction of protein pocket druggability and protein-ligand binding kinetics
• Molecular Dynamics methods for prediction of relative drug-protein binding kinetics
• Enhanced Molecular Dynamics methods: modeling of slow protein dynamics and prediction of transient pockets in proteins
• Thermodynamics and kinetics of ligand-protein binding, entropy of biomolecular systems.
• Protein adsorption on inorganic surfaces, force fields for modeling of bio-inorganic interface.

Developed Software

• τRAMD – prediction of relative protein-ligand residence times
  • MD-based computational workflow https://www.h-its.org/downloads/ramd/
  • ML approach for analysis of τRAMD Trajectories https://zenodo.org/record/3240554#.XUrgNkOxU5k
• TRAPP – TRAnsient Pockets in Protein – http://www.mcm.h-its.org/trapp
  • program package for simulation, analysis, and visualization of protein cavity dynamics and for detection of transient sub-pockets using protein motion trajectories or ensembles of protein structures.
• L-RIP & RIPlig  – http://mcm.h-its.org/lrip-riplig
  •  two non-equilibrium MD approaches aimed at identification of slow conformational changes of a protein binding site
• ProMetCS – protein-metal continuum solvent force field; implemented in SDA – Simulation of Diffusional Association packet – http://mcm.h-its.org/sda7

Education

Ph.D. in Physics and Mathematics, St. Petersburg State University, Russia

Professional experience

2009-present  Molecular and Cellular Modeling Group of Prof. R.C. Wade, HITS, Heidelberg, Germany
2002-2009  Theoretical Chemistry group of Prof. R. J. Buenker; Wuppertal University, Germany
2000-2002  Fellow of the Alexander von Humboldt Foundation. Theoretical Chemistry group of Prof. R. J. Buenker, Wuppertal University, Germany 2000-2002 1995-2000 Group of Molecular Photonics Prof. I.P.Vinogradov; Physics Dept. St. Petersburg University, Russia

Publications

see Google Scholar