(Q43136211)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

title

Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

0 references

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

4

Türkan Haliloğlu

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

author name string

Nevra Özer

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Celia A Schiffer

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

publication date

11 January 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

Evolutionary Applications

29 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

volume

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

page(s)

185-198

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern.

29 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Structural dynamics flexibility informs function and evolution at a proteome scale

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Effects of HIV-1 protease on cellular functions and their potential applications in antiretroviral therapy

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Elastic network normal modes provide a basis for protein structure refinement

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Sequence evolution correlates with structural dynamics

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

On the role of frustration in the energy landscapes of allosteric proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Rationale for More Diverse Inhibitors in Competition with Substrates in HIV-1 Protease

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

An integrated view of molecular coevolution in protein-protein interactions

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Global dynamics of proteins: bridging between structure and function

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Co-evolution and co-adaptation in protein networks

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Targeting structural flexibility in HIV-1 protease inhibitor binding

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Residues crucial for maintaining short paths in network communication mediate signaling in proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Ensemble-based convergence analysis of biomolecular trajectories

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Evolvability is a selectable trait

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Simulating protein evolution in sequence and structure space

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Exploring the range of protein flexibility, from a structural proteomics perspective

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Implications of protein flexibility for drug discovery

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Anisotropy of fluctuation dynamics of proteins with an elastic network model

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Approaches to the design of effective HIV-1 protease inhibitors

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Second locus involved in human immunodeficiency virus type 1 resistance to protease inhibitors

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Structure-based inhibitors of HIV-1 protease

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Comparison of the HIV-1 and HIV-2 proteinases using oligopeptide substrates representing cleavage sites in Gag and Gag-Pol polyproteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

The Protein Data Bank: a computer-based archival file for macromolecular structures

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Temperature dependence of fluctuations in HIV1-protease.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Native-state dynamics of the ubiquitin family: implications for function and evolution

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Combating susceptibility to drug resistance: lessons from HIV-1 protease.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Effect of sequence polymorphism and drug resistance on two HIV-1 Gag processing sites.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Flexibility and function in HIV-1 protease

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319865

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

15 August 2018

1 reference

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

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

21 January 2018

1 reference

A coarse grained model for the dynamics of flap opening in HIV-1 protease

21 January 2018

1 reference

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

21 January 2018

1 reference

12 December 2020

Functional modes of proteins are among the most robust

1 reference

12 December 2020

Polymorphism of HIV type 1 gag p7/p1 and p1/p6 cleavage sites: clinical significance and implications for resistance to protease inhibitors

1 reference

12 December 2020

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model

1 reference

12 December 2020

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

1 reference

12 December 2020

Principal components of the protein dynamical transition

1 reference

12 December 2020

Evolutionary conservation of protein vibrational dynamics

1 reference

12 December 2020

Identifiers

DOI

10.1111/EVA.12241

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

release_mbdszamzn5g2nhzktmmz5kxfce

29 February 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/mbdszamzn5g2nhzktmmz5kxfce

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

PubMed publication ID

25685193

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25685193%20AND%20SRC:MED&resulttype=core&format=json