(Q36218072)

12 August 2017

Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case (English)

1 reference

12 August 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Heather A Carlson

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

author name string

Phani Ghanakota

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Sarah E Graham

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Katrina W Lexa

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

publication date

19 September 2015

1 reference

12 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

volume

105

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

page(s)

21-34

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases

2 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Parameter choice matters: validating probe parameters for use in mixed-solvent simulations.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Improving protocols for protein mapping through proper comparison to crystallography data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Full protein flexibility is essential for proper hot-spot mapping.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Fragment-Based Screen against HIV Protease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Computational fragment-based binding site identification by ligand competitive saturation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Binding site detection and druggability index from first principles.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Formation and transfer of disulphide bonds in living cells

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Computational mapping identifies the binding sites of organic solvents on proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Experimental and computational mapping of the binding surface of a crystalline protein

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Structural and kinetic analysis of drug resistant mutants of HIV-1 protease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Analysis of the binding surfaces of proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

X-ray studies on cross-linked lysozyme crystals in acetonitrile-water mixture

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Locating and characterizing binding sites on proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Molecular recognition of cyclic urea HIV-1 protease inhibitors

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Discovering high-affinity ligands for proteins: SAR by NMR

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

VMD: visual molecular dynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

A novel, picomolar inhibitor of human immunodeficiency virus type 1 protease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Essential dynamics of proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Active human immunodeficiency virus protease is required for viral infectivity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Human immunodeficiency virus proteinase dimer as component of the viral polyprotein prevents particle assembly and viral infectivity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Activity and dimerization of human immunodeficiency virus protease as a function of solvent composition and enzyme concentration

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Drug pressure selected mutations in HIV-1 protease alter flap conformations

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Multiple solvent crystal structures: probing binding sites, plasticity and hydration

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Interactive essential dynamics

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Dynamite: a simple way to gain insight into protein motions.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Knowledge-based scoring function to predict protein-ligand interactions.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Functionality maps of binding sites: a multiple copy simultaneous search method

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623995

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

22 September 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3

21 January 2018

1 reference

Identification of the druggable concavity in homology models using the PLB index

21 January 2018

1 reference

12 December 2020

Organic solvents identify specific ligand binding sites on protein surfaces

1 reference

12 December 2020

Use of amino acid composition to predict ligand-binding sites

1 reference

12 December 2020

Binding MOAD (Mother Of All Databases)

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps

1 reference

12 December 2020

Identifiers

DOI

10.1002/BIP.22742

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26385317%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

PubMed publication ID

26385317

1 reference