title: 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.
authors.affiliation: Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA.
authors.forename: Srinivas Niranj
authors.initials: SN
authors.lastname: Chandrasekaran
authors.affiliation: Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA.
authors.forename: Jhuma
authors.initials: J
authors.lastname: Das
authors.affiliation: Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA.
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
authors.affiliation: Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA.
authors.forename: Charles W
authors.initials: CW
authors.lastname: Carter