(Q30501558)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

title

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

molecular dynamics simulation

3 February 2020

main subject

0 references

author

Gianni de Fabritiis

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

author name string

Ignasi Buch

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

Toni Giorgino

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

language of work or name

English

0 references

publication date

6 June 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

3 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

volume

108

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

page(s)

10184-10189

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

issue

25

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

3 February 2020

molecular dynamics simulation

1 reference

Enhanced modeling via network theory: Adaptive sampling of Markov state models

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

The free energy landscape of small molecule unbinding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Predicting novel binding modes of agonists to β adrenergic receptors using all-atom molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Induced effects of sodium ions on dopaminergic G-protein coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

High-throughput all-atom molecular dynamics simulations using distributed computing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Progress and challenges in the automated construction of Markov state models for full protein systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Conformational variability of benzamidinium-based inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Computations of standard binding free energies with molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Molecular Mechanism of Thioflavin-T Binding to the Surface of β-Rich Peptide Self-Assemblies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Mechanism of fast peptide recognition by SH3 domains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Transition networks for modeling the kinetics of conformational change in macromolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Flexible docking in solution using metadynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Biochemical mechanisms of drug action: what does it take for success?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Development and testing of a general amber force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

The many roles of computation in drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Hit and lead generation: beyond high-throughput screening

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

Evaluation of catalytic free energies in genetically modified proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121846

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Bond or cage effect: how nitrophorins transport and release nitric oxide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Receptor rigidity and ligand mobility in trypsin-ligand complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Markov models of molecular kinetics: generation and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1103547108

Why you should be using more SPR biosensor technology

21 January 2018

1 reference

12 December 2020

The use of proflavin as an indicator in temperature-jump studies of the binding of a competitive inhibitor to trypsin

1 reference

12 December 2020

STUDIES ON THE ACTIVE CENTER OF TRYPSIN. THE BINDING OF AMIDINES AND GUANIDINES AS MODELS OF THE SUBSTRATE SIDE CHAIN

1 reference

12 December 2020

The role of binding kinetics in therapeutically useful drug action

1 reference

12 December 2020

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1103547108

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646537%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

1 reference