Lahore University of Management Sciences Lahore University of Management Sciences

Computational Structural Biology

Dr. Kamran Haider

The Computational Biology group has two-fold objectives: (1) application of available computational biology techniques on various problems in biological research; (2) development of new approaches to address some challenging problems in modelling biological systems. We are primarily interested in molecular modelling methods of virtual screening that assist early-stage drug discovery. Earlier we developed a forcefield-based protocol (a combined MCSS MM-GB/SA approach) to predict small-molecule fragment binding to protein active sites. The encouraging results from this method led us to investigating further extensions of this method, for example, predicting and evaluating hydration sites in binding pockets which play crucial role in binding thermodynamics. A reliable approach for predicting binding affinities of ligands relies on accurate modelling of hydration effects.

The application of virtual screening methods is being carried out on systems of pharamceutical and agro-chemical interest such as insect Nicotinic Acetylcholine Receptors (nAChR’s) and HCV NS3 protease. We are collaborating with other groups at national and international levels to pursue our research interests in these areas.

We also intend to address the training needs of Pakistan’s scientific community in the area of bioinformatics through summer workshops that are currently being planned.

Publications

  • Haider M.K., Bertrand, H-O., Hubbard R.E., Predicting fragment binding using a combined MCSS-MMGBSA approach. J. Chem Inf. Model. 51(5), 1092-1105 (2011)
  • Hubbard R.E., Haider M.K. Hydrogen bonds in proteins: role and strength. ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons Ltd, Chichester. http://www.els.net
  • Sabbadin F., Jackson R., Haider M.K., Tampi G., Turkenburg J.P., Hart S., Bruce N.C., Grogan. G. The 1.5­A structure of XplA-heme, an unusual cytochrome P450 heme domain that catalyzes reductive biotransformation of royal demolition explosive. J. Biol. Chem. 284(41), 28467-75 (2009).