4.6 Article

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Multidisciplinary

Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations

Tang-Qing Yu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Editorial Material Biochemistry & Molecular Biology

Foundations of Biomolecular Modeling

William L. Jorgensen

Article Physics, Mathematical

DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

Lane W. Votapka et al.

COMMUNICATIONS IN COMPUTATIONAL PHYSICS (2013)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Review Cell Biology

Calculating kinetics and pathways of protein-ligand association

Martin Held et al.

EUROPEAN JOURNAL OF CELL BIOLOGY (2012)

Article Chemistry, Physical

Unassisted Transport of N-Acetyl-L-tryptophanamide through Membrane: Experiment and Simulation of Kinetics

Alfredo E. Cardenas et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

Article Biochemistry & Molecular Biology

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

Arren Bar-Even et al.

BIOCHEMISTRY (2011)

Article Chemistry, Physical

Markov state models based on milestoning

Christof Schuette et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Markov models of molecular kinetics: Generation and validation

Jan-Hendrik Prinz et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Multidisciplinary

Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations

Naveen Michaud-Agrawal et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Chemistry, Physical

Revisiting and Computing Reaction Coordinates with Directional Milestoning

Serdal Kirmizialtin et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2011)

Article Chemistry, Multidisciplinary

How Does a Drug Molecule Find Its Target Binding Site?

Yibing Shan et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Multidisciplinary Sciences

Pathway and mechanism of drug binding to G-protein-coupled receptors

Ron O. Dror et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Computer Science, Interdisciplinary Applications

Browndye: A software package for Brownian dynamics

Gary A. Huber et al.

COMPUTER PHYSICS COMMUNICATIONS (2010)

Article Chemistry, Physical

Milestoning without a Reaction Coordinate

Peter Majek et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Review Biochemical Research Methods

Everything you wanted to know about Markov State Models but were afraid to ask

Vijay S. Pande et al.

METHODS (2010)

Article Multidisciplinary Sciences

Atomically detailed simulation of the recovery stroke in myosin by Milestoning

Ron Elber et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Chemistry, Physical

Markovian milestoning with Voronoi tessellations

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

On the assumptions underlying milestoning

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Coarse master equations for peptide folding dynamics

Nicolae-Viorel Buchete et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Biochemistry & Molecular Biology

Very fast prediction and rationalization of pKa values for protein-ligand complexes

Delphine C. Bas et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Chemistry, Physical

Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide

Anthony M. A. West et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase

Ricardo J. F. Branco et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Designing calcium-sensitizing mutations in the regulatory domain of cardiac troponin C

SB Tikunova et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2004)

Article Chemistry, Physical

Computing time scales from reaction coordinates by milestoning

AK Faradjian et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Physical

Describing protein folding kinetics by molecular dynamics simulations. 1. Theory

WC Swope et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

Review Cell Biology

Structural based insights into the role of troponin in cardiac muscle pathophysiology

MX Li et al.

JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY (2004)

Article Chemistry, Physical

A simple polarizable model of water based on classical Drude oscillators

G Lamoureux et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Multidisciplinary Sciences

Electrostatics of nanosystems: Application to microtubules and the ribosome

NA Baker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)