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:

Scripts available to assess the effective sample size and de-correlation time of trajectories. See Software Page.

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

 

 

 
Recent Work:

  • "On the structural convergence of biomolecular simulations by determination of the effective sample size," E. Lyman and D.M. Zuckerman (J. Phys. Chem. B, 111:12876-12882 (2007).) (click here for PDF)

  • "Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model" F.M. Ytreberg, S.Kh. Aroutiounian and D.M. Zuckerman (J. Chem. Theory Comp., 3:1860-1866 (2007).) (click here for PDF)

  • "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin," Bin W. Zhang, David Jasnow, and Daniel M. Zuckerman (Proc. Nat. Acad. Sci. USA, 104:18043-18048 (2007).) (click here for PDF)

  • "Annealed importance sampling of peptides," E. Lyman and D.M. Zuckerman ( J. Chem. Phys., 127:065101 (2007).) (click here for PDF)

  • "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)

  • "A black-box re-weighting analysis can correct flawed simulation data," F.M. Ytreberg, and D.M. Zuckerman,(Proc. Nat. Acad. Sci. USA 105:7982-7987 (2008).) (click here for PDF); (Supplementary Material PDF)

  • "A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation," Daniel M. Zuckerman and Edward Lyman, J. Chem. Theory Comput. 2:1200-1202 (2006). (click here for PDF); (Erratum 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)

  • "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