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

Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V. Dokholyan, Charles W. Carter

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

Original languageEnglish (US)
Article number012101
JournalStructural Dynamics
Volume3
Issue number1
DOIs
StatePublished - Jan 1 2016

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Proteins
Structural properties
Crystal structure
Trajectories
proteins
trajectories
crystal structure
estimates

All Science Journal Classification (ASJC) codes

  • Radiation
  • Instrumentation
  • Condensed Matter Physics
  • Spectroscopy

Cite this

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A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms. / Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.

In: Structural Dynamics, Vol. 3, No. 1, 012101, 01.01.2016.

Research output: Contribution to journalArticle

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