(Q35048158)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

title

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

author name string

Nan-jie Deng

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

Emillio Gallicchio

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

Ronald M Levy

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

language of work or name

English

0 references

publication date

25 May 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

Journal of the American Chemical Society

31 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

volume

133

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

issue

24

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

page(s)

9387-9394

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations

31 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Fragment-Based Screen against HIV Protease

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Trapping moving targets with small molecules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Transition networks for modeling the kinetics of conformational change in macromolecules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Targeting structural flexibility in HIV-1 protease inhibitor binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

"Wide-open" 1.3 A structure of a multidrug-resistant HIV-1 protease as a drug target

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Long-timescale simulation methods

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Protein folding pathways from replica exchange simulations and a kinetic network model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Kinetic and thermodynamic characterization of HIV-1 protease inhibitors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Relationships between structure and interaction kinetics for HIV-1 protease inhibitors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Structural biology of HIV.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Active human immunodeficiency virus protease is required for viral infectivity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Folding pathways and rates for the three-stranded beta-sheet peptide Beta3s using discrete path sampling.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Temperature weighted histogram analysis method, replica exchange, and transition paths.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

The binding energetics of first- and second-generation HIV-1 protease inhibitors: implications for drug design

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116037

Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors

9 December 2018

1 reference

12 December 2020

Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function

1 reference

12 December 2020

Crucial roles of the subnanosecond local dynamics of the flap tips in the global conformational changes of HIV-1 protease

1 reference

12 December 2020

Solvation influences flap collapse in HIV-1 protease

1 reference

12 December 2020

Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA2008032

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21561098%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

1 reference