(Q42722437)

English

Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

scientific article published on 21 November 2013

In more languages

default for all languages

No label defined

No description defined

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers (English)

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

transmembrane protein

0 references

3

object named as

Wonpil Im

1 reference

Europe PubMed Central

5 November 2017

PMC publication ID

author name string

Pai-Chi Li

1

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

Naoyuki Miyashita

2

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

Satoshi Ishido

4

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

Yuji Sugita

5

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

language of work or name

1 reference

based on heuristic

inferred from title

publication date

21 November 2013

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

Journal of Computational Chemistry

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

35

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

4

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

300-308

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Architecture and membrane interactions of the EGF receptor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Membrane protein native state discrimination by implicit membrane models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Dimeric structure of the transmembrane domain of glycophorin a in lipidic and detergent environments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K⁺ channels, and integrin receptors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Cell adhesion: integrating cytoskeletal dynamics and cellular tension

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Left-Handed Dimer of EphA2 Transmembrane Domain: Helix Packing Diversity among Receptor Tyrosine Kinases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

A glycophorin A-like framework for the dimerization of photosynthetic core complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Structure of an integrin IIb 3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

The structure and function of G-protein-coupled receptors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

CHARMM: the biomolecular simulation program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

The structure of the integrin alphaIIbbeta3 transmembrane complex explains integrin transmembrane signalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Spatial Structure and pH-dependent Conformational Diversity of Dimeric Transmembrane Domain of the Receptor Tyrosine Kinase EphA1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

GxxxG motifs within the amyloid precursor protein transmembrane sequence are critical for the etiology of Abeta42.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Insertion and assembly of membrane proteins via simulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

OPM: orientations of proteins in membranes database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Transmembrane proteins in the Protein Data Bank: identification and classification.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

The GxxxG motif: a framework for transmembrane helix-helix association

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Structural basis of T cell recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Effective energy function for proteins in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Theory of protein folding: the energy landscape perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

A transmembrane helix dimer: structure and implications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Theoretical Studies of Protein Folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Signal transduction by receptors with tyrosine kinase activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

27 May 2018

Transmembrane helix assembly by window exchange umbrella sampling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Two-dimensional replica exchange approach for peptide-peptide interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Effective energy function for proteins in lipid membranes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Structure of the transmembrane dimer interface of glycophorin A in membrane bilayers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4083740

16 August 2018

Replica-exchange molecular dynamics method for protein folding

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

Stochastic Problems in Physics and Astronomy

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

A Novel Scoring Function for Predicting the Conformations of Tightly Packed Pairs of Transmembrane α-Helices

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

Prediction of transmembrane helix configurations by replica-exchange simulations

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

Multidimensional replica-exchange method for free-energy calculations

1 reference

https://api.crossref.org/works/10.1002%2FJCC.23494

21 January 2018

Implementation and application of helix-helix distance and crossing angle restraint potentials

1 reference

https://pubmed.ncbi.nlm.nih.gov/24258786

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential

1 reference

https://pubmed.ncbi.nlm.nih.gov/24258786

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/JCC.23494

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

DBLP publication ID

journals/jcc/LiMIIS14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

5 November 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q42722437&oldid=2166474556"