(Q33632614)

28 July 2017

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title

Investigating protein dynamics in collective coordinate space (English)

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28 July 2017

Kitao A

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28 July 2017

Go N

series ordinal

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28 July 2017

publication date

1 April 1999

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Current Opinion in Structural Biology

28 July 2017

published in

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28 July 2017

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28 July 2017

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28 July 2017

page(s)

164-169

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Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation

28 July 2017

cites work

1 reference

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7 January 2021

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

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7 January 2021

Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme

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7 January 2021

Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data

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7 January 2021

Essential dynamics of proteins

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7 January 2021

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space

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7 January 2021

Effect of solvent on collective motions in globular protein.

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7 January 2021

The consistency of large concerted motions in proteins in molecular dynamics simulations

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7 January 2021

Collective variable description of native protein dynamics

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7 January 2021

Quasi-harmonic method for studying very low frequency modes in proteins.

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7 January 2021

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

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7 January 2021

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

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7 January 2021

Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory

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7 January 2021

Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme

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7 January 2021

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

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7 January 2021

Optimal protocol and trajectory visualization for conformational searches of peptides and proteins

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7 January 2021

Large-amplitude nonlinear motions in proteins

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7 January 2021

Dynamics and relative stabilities of parallel- and antiparallel-stranded DNA duplexes

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7 January 2021

The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water

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7 January 2021

Internal motions of native lysozyme are more organized than those of mutants: a principal component analysis of molecular dynamics data

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7 January 2021

Characterizing global substates of myoglobin

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7 January 2021

Langevin modes of macromolecules: applications to crambin and DNA hexamers

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7 January 2021

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

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7 January 2021

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

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7 January 2021

Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem

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7 January 2021

Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.

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7 January 2021

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

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7 January 2021

Structural basis of hierarchical multiple substates of a protein. I: Introduction

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7 January 2021

Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization

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7 January 2021

Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations

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7 January 2021

Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations

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7 January 2021

Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations

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7 January 2021

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis

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7 January 2021

Multi-basin dynamics of a protein in a crystal environment

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7 January 2021

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

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7 January 2021

Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins.

1 reference

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7 January 2021

An efficient method for sampling the essential subspace of proteins.

1 reference

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7 January 2021

Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm

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7 January 2021

On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor

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https://api.crossref.org/works/10.1016%2FS0959-440X%2899%2980023-2

7 January 2021

Collective NMR relaxation model applied to protein dynamics

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7 January 2021

10.1016/S0959-440X(99)80023-2

Identifiers

DOI

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28 July 2017

1 reference