Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

Research

 

Our research areas include:

  • coarse-grained modeling and multiscale modeling of proteins and their complexes
  • prediction of protein structure: from comparative modeling to de novo folding
  • simulations of protein dynamics
  • prediction of protein interactions/ molecular docking
  • bioinformatics and biological statistics
  • computer aided drug design/ structure-based drug design
  • modeling and predicting of biomacromolecular interactions: prediction of protein function
  • development of software for molecular modeling and computational analysis of experimental data on biomacromolecules

 

 Short presentation of our review paper on coarse-grained and multiscale modeling of proteins and protein systems (The review paper [pdf]):

 

 

 

 Our research areas illustrated by molecular simulation movies (created by our Lab members, all movies are available at our YouTube channel):

  • Molecular docking of peptides to proteins that accounts for high flexibility of both interacting molecules

The movies below presents simulations of protein-peptide molecular docking using CABS-dock web server. The server has been described in http://nar.oxfordjournals.org/content... and is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/

 

  • Modeling of protein interactions, especially involving significant changes of protein structure

The movie presents example simulation of folding and binding of an intrinsically disordered protein from the study of Kurcinski M, Kolinski A and Kmiecik S. "Mechanism of Folding and Binding of an Intrinsically Disordered Protein as Revealed by Ab Initio Simulations". Journal of Chemical Theory and Computation, doi: 10.1021/ct500287c, 2014

 

 

  • Modeling of protein flexibility

Click "Play All" in the window below to see the series of movies generated by CABS-flex web server. The CABS-flex automatically predict and visualise the flexibility of user-provided protein structure. The CABS-flex is freely accessible at http://biocomp.chem.uw.edu.pl/CABSflex/ [for details see: "CABS-flex: server for fast simulation of protein structure fluctuations" Nucl Acids Res, 2013].

 

 

  • Modeling of peptide-protein docking

In the movie below, the peptide (TRAP220 coactivator) searches the surface of the protein (Retinoid X Receptor alpha) and finally binds to the specific binding site. The simulation was conducted with a fully flexible peptide (11 residues) and a moderately flexible protein (238 residues) whose conformation was restrained to near-native fluctuations [for details see: "Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidJ Steroid Biochem Mol Biol, 2010].

 

 

  • Modeling of protein folding

The movie below presents folding mechanism of the B1 Domain of Protein G (56-residue protein) [for details see: "Folding pathway of the b1 domain of protein G explored by multiscale modeling" Biophys J, 2008].

 

 

  • Modeling of small molecules

Click "Play All" in the window below to see the series of movies showing "real-time" molecular dynamics simulated within Biodesigner software. The movies and Biodesigner software were created by Piotr Rotkiewicz, former member of our labTo read description of the displayed simulations, drag the mouse over the window, and click "i" icon in the upper-right corner.

 

 

 see also Bio Comp Pictures youtube channel (shows molecular simulation movies related to the laboratory work).