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| Statistical
Mechanics Of Proteins |
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| 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. |
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| NEW: |
The Ensemble Protein Database (EPDB) The EPDB offers ensembles of structures, generated by computation, freely. Biology requires multiple conformations, afterall. |
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| Recent Work: |
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"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
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"Ensemble based convergence analysis of biomolecular
trajectories," E. Lyman and D.M. Zuckerman, Biophysical Journal,
91:164-172(2006). (click
here for PDF)
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"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)
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"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)
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“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)
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