(Q28475755)

April 2022 Public Data File from Crossref

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Comparison of multiple Amber force fields and development of improved protein backbone parameters

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Scalable molecular dynamics with NAMD

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

From Levinthal to pathways to funnels

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Mapping the protein universe

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Protein folding funnels: a kinetic approach to the sequence-structure relationship

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Canonical sampling through velocity rescaling

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Long-timescale molecular dynamics simulations of protein structure and function.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

The folding free-energy surface of HIV-1 protease: insights into the thermodynamic basis for resistance to inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

High temperature unfolding simulations of the TRPZ1 peptide

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

HIV-1 protease folding and the design of drugs which do not create resistance

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Insight into the folding inhibition of the HIV-1 protease by a small peptide

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Protein folding-simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Novel strategies for targeting the dimerization interface of HIV protease with cross-linked interfacial peptides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Escaping free-energy minima

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Protein folding and unfolding at atomic resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Targeting the HIV-protease in AIDS therapy: a current clinical perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

A simple model for calculating the kinetics of protein folding from three-dimensional structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

A theoretical search for folding/unfolding nuclei in three-dimensional protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Drug resistance mutations can effect dimer stability of HIV-1 protease at neutral pH.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Folding funnels and energy landscapes of larger proteins within the capillarity approximation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Engineering of stable and fast-folding sequences of model 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=2954147

Navigating the folding routes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

Folded monomer of HIV-1 protease

29 September 2017

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Fluctuating partially native-like topologies in the acid denatured ensemble of autolysis resistant HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Urea-dependent unfolding of HIV-1 protease studied by circular dichroism and small-angle X-ray scattering

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

A folding inhibitor of the HIV-1 protease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Molecular dynamics simulations of HIV-1 protease monomer: Assembly of N-terminus and C-terminus into beta-sheet in water solution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Flexibility and function in HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Least squares quantization in PCM

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

The molecular evolution of HIV-1 protease simulated at atomic detail.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Protein Folding in Contact Map Space

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013208

Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2954147

An alternative strategy for inhibiting multidrug-resistant mutants of the dimeric HIV-1 protease by targeting the subunit interface

27 November 2018

1 reference

12 December 2020

Enhanced sampling in the well-tempered ensemble

1 reference

12 December 2020

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

1 reference

12 December 2020

Interflap distances in HIV-1 protease determined by pulsed EPR measurements

1 reference

12 December 2020

A cooperative folding unit in HIV-1 protease. Implications for protein stability and occurrence of drug-induced mutations

1 reference

12 December 2020