(Q40216600)

18 September 2017

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase (English)

1 reference

18 September 2017

1 reference

Guohui Li

1

1 reference

PMCID

1302332

18 September 2017

Qiang Cui

series ordinal

2

1 reference

PMCID

1302332

18 September 2017

language of work or name

English

0 references

publication date

1 November 2002

1 reference

18 September 2017

18

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

18 September 2017

83

1 reference

18 September 2017

2457-2474

1 reference

18 September 2017

5

1 reference

18 September 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Time-dependent quantum methods for large systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Intrinsic flexibility and gating mechanism of the potassium channel KcsA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Flexibility and packing in proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Energetic optimization of ion conduction rate by the K+ selectivity filter

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

What the structure of a calcium pump tells us about its mechanism

22 September 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

22 September 2017

https://pubmed.ncbi.nlm.nih.gov/12414680

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Effective energy functions for protein structure prediction.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Structural basis for initiation of transcription from an RNA polymerase-promoter complex

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

VMD: visual molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Structural organization, ion transport, and energy transduction of P-type ATPases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Three-dimensional cryo-electron microscopy of the calcium ion pump in the sarcoplasmic reticulum membrane

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Molecular and structural basis of target recognition by calmodulin.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Calcium-induced structural changes and domain autonomy in calmodulin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Solution structure of calcium-free calmodulin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Calcium-induced conformational transition revealed by the solution structure of apo calmodulin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Protein-nucleic acid interactions in transcription: a molecular analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Functional consequences of glutamate, aspartate, glutamine, and asparagine mutations in the stalk sector of the Ca2+-ATPase of sarcoplasmic reticulum

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

How does a calcium pump pump calcium?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Calmodulin structure refined at 1.7 A resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

On the Mechanism of ATP‐Driven Ca2+ Transport by the Calcium ATPase of Sarcoplasmic Reticulum

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Conformational change of proteins arising from normal mode calculations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

The mechanism of Ca2+ transport by sarco(endo)plasmic reticulum Ca2+-ATPases

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Binding of Ca2+ to the (Ca(2+)-Mg2+)-ATPase of sarcoplasmic reticulum: kinetic studies

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Amino-acid sequence of a Ca2+ + Mg2+-dependent ATPase from rabbit muscle sarcoplasmic reticulum, deduced from its complementary DNA sequence.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Energetics of ion conduction through the K+ channel.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Building-block approach for determining low-frequency normal modes of macromolecules.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Hinge-bending motion in citrate synthase arising from normal mode calculations.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302332

Localization of the hinge region of the Ca(2+)-ATPase of sarcoplasmic reticulum using resonance energy transfer

2 December 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

Collective NMR relaxation model applied to protein dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

A mechanism for rotamase catalysis by the FK506 binding protein (FKBP)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

A fast algorithm for particle simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

Calcium ATPase of sarcoplasmic reticulum has four binding sites for calcium

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

Simulation of activation free energies in molecular systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

Molecular dynamics of ferrocytochrome c

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

7 January 2021

2 references

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

7 January 2021

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

inferred from DOI database lookup

7 January 2021

based on heuristic

Structure of the calcium pump from sarcoplasmic reticulum at 8-Å resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975257-0

10.1016/S0006-3495(02)75257-0

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

1302332