A consensus view of protein dynamics (Q24682188)

7

0 references

Adam Hospital

object named as

Adam Hospital

6

1 reference

ORCID Public Data File 2021

Modesto Orozco

8

object named as

Modesto Orozco

0 references

author name string

Manuel Rueda

1

0 references

Carles Ferrer-Costa

2

0 references

Alberto Pérez

4

0 references

Jordi Camps

Proceedings of the National Academy of Sciences of the United States of America

5

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language of work or name

English

0 references

publication date

16 January 2007

0 references

published in

0 references

volume

104

0 references

issue

3

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

10

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page(s)

796-801

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Contribution of surface salt bridges to protein stability

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

All-atom empirical potential for molecular modeling and dynamics studies of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Scalable molecular dynamics with NAMD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

GROMACS: fast, flexible, and free

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Dali: a network tool for protein structure comparison

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

SCOP: a structural classification of proteins database for the investigation of sequences and structures

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Stereochemical quality of protein structure coordinates

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Molecular dynamics and protein function

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Bicycle-pedal model for the first step in the vision process

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Dynamics of folded proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

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

7 April 2017

1 reference

https://api.crossref.org/works/10.1073/PNAS.0605534104

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

22 April 2017

1 reference

https://api.crossref.org/works/10.1073/PNAS.0605534104

Comparison of simple potential functions for simulating liquid water

22 April 2017

1 reference

https://api.crossref.org/works/10.1073/PNAS.0605534104

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

22 April 2017

1 reference

https://api.crossref.org/works/10.1073/PNAS.0605534104

PROCHECK: a program to check the stereochemical quality of protein structures

22 April 2017

1 reference

https://api.crossref.org/works/10.1073/PNAS.0605534104

Scoring function for automated assessment of protein structure template quality

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

SCOP database in 2004: refinements integrate structure and sequence family data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Essential dynamics of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Simultaneous determination of protein structure and dynamics.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Force fields for protein simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Molecular dynamics simulations of biomolecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Cooperativity in drug-DNA recognition: a molecular dynamics study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

Investigating the local flexibility of functional residues in hemoproteins.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1783393

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

30 May 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605534104

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605534104

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605534104

Urea parametrization for molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605534104

21 January 2018

1 reference

12 December 2020

Stabilization of Proteins by Ligand Binding: Application to Drug Screening and Determination of Unfolding Energetics

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

The dynamics of proteins

1 reference

12 December 2020

Erythropoietin receptor activation by a ligand-induced conformation change

1 reference

12 December 2020

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0605534104

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1073/PNAS.0605534104

1 reference

journals/pnas/RuedaFMPCHGO07

0 references

1 reference

DBLP Dataset 2021-01-02

28 January 2021

2690168

1 reference

1 reference

2690168

PubMed publication ID

17215349

1 reference