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A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms.

ABSTRACT: PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH.

SUBMITTER: Chandrasekaran SN

PROVIDER: S-EPMC4769271 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms.

Chandrasekaran Srinivas Niranj SN Das Jhuma J Dokholyan Nikolay V NV Carter Charles W CW

Structural dynamics (Melville, N.Y.) 20160101 1

PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different al ...[more]

PMID: 26958584

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