Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin (Q41583765)

4 October 2017

Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin (English)

1 reference

4 October 2017

Haruki Nakamura

1 reference

4 October 2017

Bhaskar Dasgupta

1 reference

4 October 2017

Akira R Kinjo

series ordinal

1 reference

4 October 2017

language of work or name

1 reference

17 December 2012

1 reference

4 October 2017

1 reference

4 October 2017

1 reference

4 October 2017

1 reference

4 October 2017

168-178

1 reference

Dynamic features of homodimer interfaces calculated by normal-mode analysis

4 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

The Pfam protein families database

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Independent interactions of ubiquitin-binding domains in a ubiquitin-mediated ternary complex

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

In silico elucidation of the recognition dynamics of ubiquitin

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Protein binding specificity versus promiscuity.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Large‐scale comparison of protein essential dynamics from molecular dynamics simulations and coarse‐grained normal mode analyses

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Ubiquitin--molecular mechanisms for recognition of different structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Exploring functional roles of multibinding protein interfaces

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Protein structure databases with new web services for structural biology and biomedical research

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Dynamic personalities of proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Robust protein protein interactions in crowded cellular environments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Clustal W and Clustal X version 2.0

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Relating three-dimensional structures to protein networks provides evolutionary insights

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Evidence for dynamically organized modularity in the yeast protein-protein interaction network

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

A comparative study of motor-protein motions by using a simple elastic-network model

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Lethality and centrality in protein networks

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Conformational change of proteins arising from normal mode calculations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Investigating protein dynamics in collective coordinate space

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

CATH--a hierarchic classification of protein domain structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

The role of disorder in interaction networks: a structural analysis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Dynamic property is a key determinant for protein-protein interactions

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

A dissection of specific and non-specific protein-protein interfaces

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

Distinct functional surface regions on ubiquitin

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3588913

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

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPRO.2195

Specificity of molecular interactions in transient protein-protein interaction interfaces

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPRO.2195

Two folded conformers of ubiquitin revealed by high-pressure NMR

21 January 2018

1 reference

12 December 2020

Protein-protein interfaces are special

1 reference

12 December 2020

Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding

1 reference

12 December 2020

Protein structural change upon ligand binding: linear response theory

1 reference

12 December 2020

Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis

1 reference

12 December 2020

1 reference

12 December 2020

Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model

1 reference

12 December 2020

Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners

1 reference

12 December 2020

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.2195

1 reference

4 October 2017

1 reference

4 October 2017

PubMed publication ID

23169174

1 reference