(Q36179862)

12 August 2017

Sequence evolution correlates with structural dynamics (English)

1 reference

12 August 2017

2

Ivet Bahar

0 references

author name string

Ying Liu

series ordinal

1

1 reference

12 August 2017

16 March 2012

1 reference

Molecular Biology and Evolution

12 August 2017

1 reference

12 August 2017

29

1 reference

12 August 2017

2253-2263

1 reference

12 August 2017

9

1 reference

Detecting coevolving positions in a molecule: why and how to account for phylogeny

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Remote thioredoxin recognition using evolutionary conservation and structural dynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Stefin A displaces the occluding loop of cathepsin B only by as much as required to bind to the active site cleft

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

An integrated view of molecular coevolution in protein-protein interactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Global dynamics of proteins: bridging between structure and function

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Structural and functional constraints in the evolution of protein families

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Protein dynamics and conformational disorder in molecular recognition

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Linking folding and binding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Analysis of correlated mutations in HIV-1 protease using spectral clustering

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

The Pfam protein families database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Empirical fitness landscapes reveal accessible evolutionary paths

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Structure, function, and evolution of transient and obligate protein-protein interactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Antibody multispecificity mediated by conformational diversity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Structural stability of binding sites: consequences for binding affinity and allosteric effects.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Analysis of protein-protein interaction sites using surface patches

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Crystal structure of the wild-type human procathepsin B at 2.5 A resolution reveals the native active site of a papain-like cysteine protease zymogen

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Identification of common molecular subsequences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Exploration of the relationship between topology and designability of conformations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

An interdomain sector mediating allostery in Hsp70 molecular chaperones

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Metal-binding sites are designed to achieve optimal mechanical and signaling properties

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Evolutionary expansion and specialization of the PDZ domains

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

oGNM: online computation of structural dynamics using the Gaussian Network Model

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Investigating the local flexibility of functional residues in hemoproteins.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Cation-pi interactions in protein-protein interfaces

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424413

Gaussian Dynamics of Folded Proteins

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS097

Emergence of Preferred Structures in a Simple Model of Protein Folding

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS097

Amino-Acid Properties and Consequences of Substitutions

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS097

Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22427707

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Role of the occluding loop in cathepsin B activity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22427707

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSS097

1 reference

12 August 2017

1 reference

12 August 2017

1 reference

PMCID

3424413