Daniel M Zuckerman, Assistant Professor      

Statistical Mechanics Of Proteins
   
The Zuckerman group develops algorithms and software for understanding the molecular basis of protein behavior -  especially large conformational changes and binding events.  Principles of statistical mechanics underpin the group's efforts to develop rigorous, but fast, methods for calculating free energies of binding and to gain understanding of activated transitions in proteins and molecular systems generally.

 

 

 
NEW:  The Ensemble Protein Database (EPDB) The EPDB offers ensembles of structures, generated by computation, freely. Biology requires multiple conformations, afterall.
 

 

 

Recent Work:
  • "Comparison of free energy methods for molecular systems," F.M. Ytreberg, R.H. Swendsen, and D.M. Zuckerman, J. Chem. Phys 125:184114 (2006). (click here for PDF)

  • BlackBox Reweighting," F.M. Ytreberg, and D.M. Zuckerman, preprint Pdf

  • "Ensemble based convergence analysis of biomolecular trajectories," E. Lyman and D.M. Zuckerman, Biophysical Journal, 91:164-172(2006). (click here for PDF)

  • "Resolution Exchange Simulation with Incremental Coarsening," E. Lyman and D. M. Zuckerman, J. Chem. Theory Comp., 2:656-666 (2006). (click here for PDF) (click here for correction)

  • "Resolution Exchange Simulation," E. Lyman, F. M. Ytreberg, and D. M. Zuckerman, Physical Review Letters, Phys. Rev. Lett. 96:028105 (2006). (click here for PDF)

  • “Simple estimation of absolute free energies for biomolecules,”  F.M. Ytreberg and D.M. Zuckerman, J. Chem. Phys., 124:104105 (2006). (click here for PDF)

   
   
   
   
   

University of Pittsburgh Department of Computational Biology