(Q34181379)

31 July 2017

Molecular dynamics simulations of peptides and proteins with amplified collective motions (English)

1 reference

31 July 2017

2

Yunyu Shi

1 reference

31 July 2017

Zhiyong Zhang

1

1 reference

PubMed ID

12770868

31 July 2017

Haiyan Liu

series ordinal

3

1 reference

PubMed ID

12770868

31 July 2017

language of work or name

English

0 references

publication date

1 June 2003

1 reference

31 July 2017

1 reference

31 July 2017

84

1 reference

31 July 2017

3583-3593

1 reference

31 July 2017

6

1 reference

How to describe protein motion without amino acid sequence and atomic coordinates.

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Domain movements in human fatty acid synthase by quantized elastic deformational model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Anisotropy of fluctuation dynamics of proteins with an elastic network model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Long timescale simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Collective protein dynamics in relation to function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Protein dynamics simulations from nanoseconds to microseconds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Investigating protein dynamics in collective coordinate space

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

An efficient method for sampling the essential subspace of proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Essential dynamics of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Crystallographic determination of the mode of binding of oligosaccharides to T4 bacteriophage lysozyme: Implications for the mechanism of catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

WHAT IF: a molecular modeling and drug design program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

A mutant T4 lysozyme displays five different crystal conformations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Efficient sampling in collective coordinate space.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Molecular dynamics simulation of the docking of substrates to proteins.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Prediction of protein conformational freedom from distance constraints

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302944

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Molecular dynamics with coupling to an external bath

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Protein flexibility in solution and in crystals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Predicting slow structural transitions in macromolecular systems: Conformational flooding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Gaussian Dynamics of Folded Proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Semianalytical treatment of solvation for molecular mechanics and dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Solvent mobility and the protein 'glass' transition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975090-5

Energy landscape of a native protein: jumping-among-minima model

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12770868

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(03)75090-5

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

12770868