(Q37019487)

17 August 2017

Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis (English)

1 reference

17 August 2017

Martin Karplus

1 reference

17 August 2017

Yifei Kong

1 reference

PMC publication ID

2605193

17 August 2017

language of work or name

English

0 references

publication date

1 January 2009

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

17 August 2017

145-154

1 reference

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

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Structure of the split PH domain and distinct lipid-binding properties of the PH-PDZ supramodule of alpha-syntrophin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Functional dynamics of PDZ binding domains: a normal-mode analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

New advances in normal mode analysis of supermolecular complexes and applications to structural refinement

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Ligand-dependent dynamics and intramolecular signaling in a PDZ domain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Tandem PDZ repeats in glutamate receptor-interacting proteins have a novel mode of PDZ domain-mediated target binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Organization of signaling complexes by PDZ-domain scaffold proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

PDZ Domain Proteins: Plug and Play!

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Syntrophins and dystrobrevins: defining the dystrophin scaffold at synapses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

An efficient algorithm for large-scale detection of protein families

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

PDZ domains: structural modules for protein complex assembly

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

PDZ domains and the organization of supramolecular complexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Evolutionarily conserved pathways of energetic connectivity in protein families

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

PDZ domains: fundamental building blocks in the organization of protein complexes at the plasma membrane

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Canonical dynamics: Equilibrium phase-space distributions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Localization of postsynaptic density-93 to dendritic microtubules and interaction with microtubule-associated protein 1A

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

VMD: visual molecular dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

PDZ Domains and the Formation of Protein Networks at the Plasma Membrane

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2605193

Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18618698

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The signaling pathway of rhodopsin

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18618698

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Molecular dynamics simulations at constant pressure and/or temperature

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.22139

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.22139

Constant pressure molecular dynamics for molecular systems

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.22139

Identifiers

DOI

10.1002/PROT.22139

1 reference

17 August 2017

1 reference

PMC publication ID

2605193

17 August 2017

PubMed publication ID

18618698

1 reference

PMC publication ID

2605193