DESCRIPTION OF THE GROUP

This group focuses on research on proteins, especially in cellular membranes. These studies regard, among others, mechanism of GPCR receptors activation (G-protein-coupled receptors) and functioning of molecular switches in the above mentioned receptors. Biomodeling enables group members to predict ligand activity, in order to design appropriate selective drugs.

The second scientific interest of this group is research on structure and dynamics of proteins forming γ-secretase complex. Models of interaction between these proteins may help to understand the role of mutations causing Alzheimer’s disease and to clarify, which structural modifications in the substrate-binding site influence the change of the cutting place and formation of toxic β-amyloid (Aβ42).


GROUP MEMBERS

Professor Sławomir Filipek

THE LEADER OF THE GROUP

TEAM

Professor Sławomir Filipek,
Faculty of Chemistry and Biological and Chemical Research Centre
of the University of Warsaw,
e-mail:sfilipek@chem.uw.edu.pl
phone:+48-22-5526545; +48-22-5526405,
room number 2.36

Dorota Latek Ph.D.,
Anna Modzelewska Ph.D.,
Przemysław Miszta Ph.D.,
Aleksander Dębiński M.Sc.,
Krzysztof Młynarczyk M.Sc.,
Wojciech Puławski M.Sc.,
Paweł Pasznik M.Sc.,
Jakub Jakowiecki M.Sc.,
common phone number: +48-22-5526545; room number 2.36

RESEARCH ACTIVITIES

Moreover, this group works on design of medicines aimed at various molecular targets, and on interactions of proteins with graphene, carbon nanotubes and other electrode materials for biosensors.

Research also includes computer modeling of:

  • Mechanisms of protein functioning,
  • Interactions between proteins and ligands (chemical compounds or peptide ligands),
  • Formation of protein-protein complexes,
  • Influence of ligands on proteins in cellular membrane.

Computing is performed mainly on powerful CPU/GPU workstations. Specification: 2 Intel Xeon multi-core processors, 2 GPU NVIDIA GeForce or Tesla cards with specialized CUDA computing platform. Workstations are equipped with monitors with 3-D function for work in polarized 3-D glasses.

Scientific software: programs for simulation of molecular dynamics: NAMD, GROMACS, CHARMM, YASARA. Programs for data preparation, result analysis and visualization: Schrödinger platform, VMD, PyMol etc. Drug-protein docking, virtual screening: LigandScout, Schrödinger platform. Computing can also be performed at supercomputing centres.

Research services

Performance of molecular dynamics simulations (all-atom and simplified: coarse-grain and implicit-solvent) for individual proteins and their complexes.

Methods of chemical compound – protein docking, virtual screening, drug design.

Range and price of research services for negotiation.