Journal ArticleDOI
Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom
Stefan Fischer,Martin Karplus +1 more
TLDR
In this paper, an algorithm is presented for determining multi-dimensional reaction coordinates between two known conformers, which is suitable for the study of complex isomerization reactions, including allosteric transitions in proteins and more general conformational changes of macromolecules.About:
This article is published in Chemical Physics Letters.The article was published on 1992-06-26. It has received 456 citations till now. The article focuses on the topics: Saddle point & Degrees of freedom.read more
Citations
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Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
Bio3d: an R package for the comparative analysis of protein structures
TL;DR: An automated procedure for the analysis of homologous protein structures has been developed that facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for theAnalysis of protein structural evolution.
Journal ArticleDOI
Simulation of activation free energies in molecular systems
TL;DR: In this article, a method for determining activation free energies in complex molecular systems is presented, which relies on knowledge of the minimum energy path and bases the activation free energy calculation on moving along this path from a minimum to a saddle point.
Journal ArticleDOI
A generalized synchronous transit method for transition state location
TL;DR: A generalized synchronous transit method for locating transition state structures or first-order saddle points was proposed in this article, which is based on the established scheme of combining the linear or quadratic synchronized transit method with conjugate gradient refinements but generalized to deal with molecular and periodic systems in a seamless manner.
Journal ArticleDOI
Simplified and improved string method for computing the minimum energy paths in barrier-crossing events.
TL;DR: A simplified and improved version of the string method, originally proposed by E et al. (2002) for identifying the minimum energy paths in barrier-crossing events, that is more stable and accurate and combined with the climbing image technique for the accurate calculation of saddle points.
References
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Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
Numerical Recipes, The Art of Scientific Computing
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