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Ensemble Protein Database (University of Pittsburgh)

EPDB:The Ensemble Protein Database Homepage. The Ensemble Protein Database. A public resource housed at the University of Pittsburgh. Department of Computational Biology. Curated by Prof. Daniel M. Zuckerman. Co-created by Prof. F. Marty Ytreberg (University of Idaho). Skip the verbiage – take me right to the structures - link. What is the “Ensemble Protein Database”? Contain ordinary molecular dynamics trajectories, however. Statistical rotamer libraries of side-chain configurations. link. Has a quite p...

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Ensemble Protein Database (University of Pittsburgh) | epdb.pitt.edu Reviews

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EPDB:The Ensemble Protein Database Homepage. The Ensemble Protein Database. A public resource housed at the University of Pittsburgh. Department of Computational Biology. Curated by Prof. Daniel M. Zuckerman. Co-created by Prof. F. Marty Ytreberg (University of Idaho). Skip the verbiage – take me right to the structures - link. What is the “Ensemble Protein Database”? Contain ordinary molecular dynamics trajectories, however. Statistical rotamer libraries of side-chain configurations. link. Has a quite p...

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Ensemble Protein Database (University of Pittsburgh) | epdb.pitt.edu Reviews

https://epdb.pitt.edu

EPDB:The Ensemble Protein Database Homepage. The Ensemble Protein Database. A public resource housed at the University of Pittsburgh. Department of Computational Biology. Curated by Prof. Daniel M. Zuckerman. Co-created by Prof. F. Marty Ytreberg (University of Idaho). Skip the verbiage – take me right to the structures - link. What is the “Ensemble Protein Database”? Contain ordinary molecular dynamics trajectories, however. Statistical rotamer libraries of side-chain configurations. link. Has a quite p...

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epdb.pitt.edu

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EPDB List (University of Pittsburgh)

http://www.epdb.pitt.edu/list.html

EPDB:The Ensemble Protein Database Ensemble List. Sets of physically and chemically reasonable structures generated using a fairly crude method, but with substantial structural diversity. ( More details. Ensemble files include computational details. Human CDC25B Catalytic Domain. Approximate path ensembles consist of all-atom configurations connecting the two indicated PDB structures. Paths were generated based on coarse-grained simulation followed by addition of atomistic detail. ( More details.

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EPDB Explanation of Types (University of Pittsburgh)

http://www.epdb.pitt.edu/types.html

EPDB:The Ensemble Protein Database Ensemble Types. Explanation of Ensemble Types. It is easiest to understand the various ensemble types by starting with the ideal – the Boltzmann ensemble. Statistical physics (a.k.a. statistical mechanics) tells us that protein conformations in solution will be distributed according to a suitable Boltzmann weighting. That is, a conformation (including protein plus solvent) denoted by x. Will occur with probability proportional to exp[–E( x. Ensembles are generated start...

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Ensemble Protein Database (University of Pittsburgh)

http://www.epdb.pitt.edu/index.html

EPDB:The Ensemble Protein Database Homepage. The Ensemble Protein Database. A public resource housed at the University of Pittsburgh. Department of Computational Biology. Curated by Prof. Daniel M. Zuckerman. Co-created by Prof. F. Marty Ytreberg (University of Idaho). Skip the verbiage – take me right to the structures - link. What is the “Ensemble Protein Database”? Contain ordinary molecular dynamics trajectories, however. Statistical rotamer libraries of side-chain configurations. link. Has a quite p...

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Zuckerman Lab

http://ccbb.pitt.edu/Faculty/zuckerman

Physical Lens on the Cell. CPCB Ph.D. Program. Physical Lens on the Cell. And a new online book. Accurate estimation of protein folding and unfolding times: Beyond Markov state models. Suárez, Ernesto; Adelman, Joshua; Zuckerman, Daniel,. Journal of Chemical Theory and Computation. Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. Estimating First Passage Time Distributions from Weighted Ensemble Simulations and non-Markovian Analyses.

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Ensemble Protein Database (University of Pittsburgh)

EPDB:The Ensemble Protein Database Homepage. The Ensemble Protein Database. A public resource housed at the University of Pittsburgh. Department of Computational Biology. Curated by Prof. Daniel M. Zuckerman. Co-created by Prof. F. Marty Ytreberg (University of Idaho). Skip the verbiage – take me right to the structures - link. What is the “Ensemble Protein Database”? Contain ordinary molecular dynamics trajectories, however. Statistical rotamer libraries of side-chain configurations. link. Has a quite p...

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