4.6 Article

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Alchemical free energy methods for drug discovery: progress and challenges

John D. Chodera et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Chemistry, Physical

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

Victor Ovchinnikov et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding

Hiroko X. Kondo et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Article Biochemical Research Methods

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

Daniel-Adriano Silva et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Chemistry, Physical

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Markovian milestoning with Voronoi tessellations

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Biochemistry & Molecular Biology

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ⇆ Closed Transitions

Oliver Beckstein et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Chemistry, Physical

Apo Adenylate Kinase Encodes Its Holo Form: A Principal Component and Varimax Analysis

Robert I. Cukier

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Chemistry, Physical

Statistically optimal analysis of samples from multiple equilibrium states

Michael R. Shirts et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Finding transition pathways using the string method with swarms of trajectories

Albert C. Pan et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Multidisciplinary Sciences

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

Kei-ichi Okazaki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemistry & Molecular Biology

The atomistic mechanism of conformational transition in adenylate kinase: A TEE-REX molecular dynamics study

Marcus B. Kubitzki et al.

STRUCTURE (2008)

Article Multidisciplinary Sciences

Intrinsic motions along an enzymatic reaction trajectory

Katherine A. Henzler-Wildman et al.

NATURE (2007)

Article Multidisciplinary Sciences

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

Karunesh Arora et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Illuminating the mechanistic roles of enzyme conformational dynamics

Jeffrey A. Hanson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Physical

On-the-fly string method for minimum free energy paths calculation

Luca Maragliano et al.

CHEMICAL PHYSICS LETTERS (2007)

Article Multidisciplinary Sciences

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

Thomas F. Miller et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

Todd J. Dolinsky et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

Conformational transitions of adenylate kinase: Switching by cracking

Paul C. Whitford et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Chemistry, Physical

Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations

John D. Chodera et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Chemistry, Physical

String method in collective variables: Minimum free energy paths and isocommittor surfaces

Luca Maragliano et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

Molecular dynamics of apo-adenylate kinase: A principal component analysis

Hongfeng Lou et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Review Biochemistry & Molecular Biology

Very fast empirical prediction and rationalization of protein pKa values

H Li et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase

P Maragakis et al.

JOURNAL OF MOLECULAR BIOLOGY (2005)

Article Chemistry, Physical

Finite temperature string method for the study of rare events

E Weinan et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Biochemistry & Molecular Biology

Associative mechanism for phosphoryl transfer: A molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates

H Krishnamurthy et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

TJ Dolinsky et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

M Wolf-Watz et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)

Article Multidisciplinary Sciences

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

O Miyashita et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Biochemistry & Molecular Biology

A novel view of domain flexibility in E-coli adenylate kinase based on structural mode-coupling 15N NMR relaxation

V Tugarinov et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Computer Science, Interdisciplinary Applications

Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations

M Souaille et al.

COMPUTER PHYSICS COMMUNICATIONS (2001)