(Q36280885)

13 August 2017

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin (English)

1 reference

13 August 2017

Caves LS

1

1 reference

PMCID

2143962

13 August 2017

Evanseck JD

series ordinal

2

1 reference

PMCID

2143962

13 August 2017

Karplus M

series ordinal

3

1 reference

13 August 2017

1 March 1998

1 reference

13 August 2017

1 reference

13 August 2017

7

1 reference

13 August 2017

649-666

1 reference

13 August 2017

3

1 reference

Calculations of nucleic acid conformations

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Proteins at atomic resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Realistic simulations of native-protein dynamics in solution and beyond

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Structural mechanisms for domain movements in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

A sampling problem in molecular dynamics simulations of macromolecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Methodological advances in molecular dynamics simulations of biological systems.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Problems in simulating macromolecular movements

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Mapping protein dynamics by X-ray diffraction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Mechanisms of cooperativity and allosteric regulation in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Accurate simulation of protein dynamics in solution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Molecular dynamics simulations in biology

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

The Energy Landscapes and Motions of Proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Thermodynamic fluctuations in protein molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

The Protein Data Bank: a computer-based archival file for macromolecular structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

An extended sampling of the configurational space of HPr from E. coli.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

An efficient method for sampling the essential subspace of proteins.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Long timestep dynamics of peptides by the dynamics driver approach.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Ligand binding to heme proteins: connection between dynamics and function

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Novel methods of sampling phase space in the simulation of biological systems

29 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

On the sensitivity of MD trajectories to changes in water-protein interaction parameters: the potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Effect of solvent on collective motions in globular protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

A discussion of the solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Conformational search by potential energy annealing: algorithm and application to cyclosporin A.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Rational choice of molecular dynamics simulation parameters through the use of the three-dimensional autocorrelation method: application to calmodulin flexibility study

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Using molecular dynamics simulations on crambin to evaluate the suitability of different continuum dielectric and hydrogen atom models for protein simulations

21 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143962

Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

21 October 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Computer simulation of protein motion

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560070314

Not just your average structures

21 January 2018

1 reference

12 December 2020

Temperature dependence of the structure and dynamics of myoglobin. A simulation approach

1 reference

12 December 2020

Conformational sampling using high-temperature molecular dynamics

1 reference

12 December 2020

First-principles calculation of the folding free energy of a three-helix bundle protein

1 reference

12 December 2020

Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study

1 reference

12 December 2020

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

1 reference

12 December 2020

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

1 reference

12 December 2020

Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme product complex

1 reference

12 December 2020

Packing structures and transitions in liquids and solids

1 reference

12 December 2020

Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics simulation

1 reference

12 December 2020

Complexity in proteins

1 reference

12 December 2020

Bio-molecular dynamics comes of age

1 reference

12 December 2020

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.5560070314

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

PMCID

2143962