Molecular Modeling

Protein/Ligand Analysis

• Docking
• Virtual Screening
• Analysis of Antonín Holý Library

Aimed at both the BIO and CHEM clusters, we offer expertise/help/advice on various aspects of (bio)molecular modeling. For biomolecules (proteins, nucleic acids, carbohydrates) of interest, analyses of their dynamics beyond experimental structural information from X-ray crystallography, NMR, or cryo-EM can be performed using molecular dynamics simulations (MD) using AMBER, GROMACS or NAMD. For organic compounds, conformational analyses, calculation of properties (energies, atomic charges, electrostatic potentials, spectra, pKa’s) and reaction mechanisms can be carried out using quantum chemical calculations in Gaussian or Turbomole. For biomolecular complexes, docking and scoring approaches give their structures and energies, respectively, and can be used in virtual screening pipelines, i.e. finding hits in virtual compound libraries for a given biomolecular target. For the lead-optimization stage, free-energy simulation protocols can be used.

Personnel

For Protein/Ligand Analysis support, drop an e-mail to Martin Lepšík. Direct general questions about the service to Hector Martinez-Seara.