(Q30618624)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

title

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

1 reference

molecular dynamics simulation

0 references

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

Anna Berteotti

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

Giovanni Bottegoni

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

Walter Rocchia

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

author name string

Andrea Cavalli

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

language of work or name

English

0 references

publication date

27 January 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

volume

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

page(s)

6155

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

28 February 2020

copyright license

start time

27 January 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Foundations of biomolecular modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Population based reweighting of scaled molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Molecular dynamics simulations and 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=4308819

Pathway and mechanism of drug binding to 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=4308819

Complete reconstruction of an enzyme-inhibitor binding process by 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=4308819

How does a drug molecule find its target binding site?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Long-lasting target binding and rebinding as mechanisms to prolong in vivo drug action

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Improved side-chain torsion potentials for the Amber ff99SB protein 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=4308819

Four generations of transition-state analogues for human purine nucleoside phosphorylase.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

MolProbity: all-atom structure validation for macromolecular crystallography

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

l -Enantiomers of Transition State Analogue Inhibitors Bound to Human Purine Nucleoside Phosphorylase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Drug-target residence time and its implications for lead optimization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

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=4308819

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=4308819

Crystal structure of human purine nucleoside phosphorylase complexed with acyclovir

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Crystal structure of human purine nucleoside phosphorylase at 2.3A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Achieving the ultimate physiological goal in transition state analogue inhibitors for purine nucleoside phosphorylase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

One-third-the-sites transition-state inhibitors for purine nucleoside phosphorylase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4308819

Identification of slow molecular order parameters for Markov model construction

20 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

From A to B in free energy space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

Single-sweep methods for free energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

The role of water in host-guest interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25625196

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A simple and fast algorithm for K-medoids clustering

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS7155

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NCOMMS7155

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

28 February 2020

ADS bibcode

2015NatCo...6.6155D

0 references

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

PubMed publication ID

25625196

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25625196%20AND%20SRC:MED&resulttype=core&format=json