Crystallochemistry laboratory

Faculty of Chemistry, University of Warsaw

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Prashant Kumar

Article Index
Prashant Kumar
Conferences & Workshops:
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Prashant Kumar


Scientific Interest:

  • Inter and Intra molecular interaction
  • X-ray crystallography
  • Computational chemisty


  • Watching documentries 
  • Going places 

Tel: +48 22 8220211

Fax: +48 22 8222892

E-Mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Funded projects:

1. PRELUDIUM 7: Structural and dynamic aspect of the electrostatic interaction in HIV-1 protease. 

HIV-1 protease, an aspartic protease of the human immunodeficiency virus (HIV), is an important target for drug design strategies to combat acquired immune deficiency syndrome (AIDS). Unfortunately, the effectiveness of new drugs is strongly limited by rapidly emerging mutations induced drug resistance. HIV-1 protease is a homodimer and the active site of the protein is formed on the border of the two monomers. We propose to examine key electrostatic interactions present in HIV-1 protease dimer ( wild type and mutant ) that stabilize the formation of the complex , using the electron density distribution reconstructed from a aspherical atom databank (UBDB) (Dominiak et al . 2007 Volkov et al .. 2007) . Research will be carried out on the basis of the HIV-1 protease structures available in  the PDB. Crystal structures will provide a starting point to conduct molecular dynamics (MD) in order to take into account in the calculation of the interaction energy dynamic aspects of interactions between monomers in the HIV-1 protease dimer. We expect that the use of Ees energy calculations carried out on the basis of the charge density distribution of multiple conformers of HIV-1 protease (wild type and  mutants) obtained from the molecular dynamics simulations (MD) will provide us with the relevant  details of the dimer stabilization and mechanisms of drug resistance. 



1. Bojarowski, S. A., Kumar, P. and Dominiak, P. M. (2016), A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation. ChemPhysChem. doi:10.1002/cphc.201600390

2. Kumar P., Bojarowski S. A.,  Jarzembska K. N., Domagała S., Vanommeslaeghe K., MacKerell A. D., Dominiak P. M.  A comparative study of transferable aspherical pseudoatom databank and classical force fields for predicting electrostatic interactions in molecular dimers.  J. Chem. Theory Comput. 2014, 10(4), pp 1652-1664.  



Conferences and Workshops:

. European Charge Density Meeting 6, Štrbské Pleso, Slovakia September 15-20, 2012

. Software Development for Crystallographers Satellite Meeting, University of Warwick, Coventry UK, August 22-24, 2013

. European Crystallography Meeting, University of Warwick, Coventry UK,  August 25-29, 2013

. EUROCUP VII, OpenEye Scientific, Méry-sur-Oise, France, May 14-16, 2014

. Visit, Lawrence Berkeley National Laboratory, Berkely, USA, September, 15-20, 2014

. AMBER Molecular Dynamics Workshop, Technion Israel Institute of Technology, Haifa, Israel, April, 26-30, 2015

. Multipole Meeting: Approack to Structural Science, Warsaw, Poland, May 10-13,2015

Konwersatorium Kystalograficzne 2015, Wrocław, Poland, June 24-26, 2015




Last Updated on Monday, 11 July 2016 11:46  

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