Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities (Q27679166)

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5 March 2020

title

Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities (English)

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4

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author name string

Sarah Barelier

1

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Sarah E Boyce

2

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Inbar Fish

3

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David B Goodin

5

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Brian K Shoichet

6

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language of work or name

English

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publication date

18 July 2013

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5 March 2020

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volume

8

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issue

7

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5 March 2020

page(s)

e69153

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Creative Commons Attribution 4.0 International

5 March 2020

copyright license

start time

18 July 2013

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Targeting conserved water molecules: design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Engineering a model protein cavity to catalyze the Kemp elimination

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

A Structure-Based Approach to Ligand Discovery for 2 C -Methyl- d -erythritol-2,4-cyclodiphosphate Synthase: A Target for Antimicrobial Therapy †

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Replacement of an Electron Transfer Pathway in Cytochrome c Peroxidase with a Surrogate Peptide † , ‡

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Hierarchical docking of databases of multiple ligand conformations

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

A model binding site for testing scoring functions in molecular docking

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Excision of a proposed electron transfer pathway in cytochromecperoxidase and its replacement by a ligand-binding channel

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Automated docking screens: a feasibility study

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

ZINC: a free tool to discover chemistry for biology

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

A hierarchical approach to all-atom protein loop prediction

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Improved protein-ligand docking using GOLD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Classical electrostatics in biology and chemistry

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Docking and scoring with ICM: the benchmarking results and strategies for improvement

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Sampling protein motion and solvent effect during ligand binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Hsp90 inhibitors and drugs from fragment and virtual screening.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

An evaluation of Poisson-Boltzmann electrostatic free energy calculations through comparison with experimental mutagenesis data.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase 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=3715451

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Solvated docking: introducing water into the modelling of biomolecular complexes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Probing molecular docking in a charged model binding site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Testing a flexible-receptor docking algorithm in a model binding site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

What makes a binding site a binding site?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Embryonic tissue differentiation in Caenorhabditis elegans requires dif-1, a gene homologous to mitochondrial solute carriers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Introduction of the transposable element mariner into the germline of Drosophila melanogaster.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Virtual screening and optimization yield low-nanomolar inhibitors of the tautomerase activity of Plasmodium falciparum macrophage migration inhibitory factor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Identification of novel adenosine A(2A) receptor antagonists by virtual screening.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Soft docking and multiple receptor conformations in virtual screening

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

The behavioral endocrinology of domestication: A comparison between the domestic guinea pig (Cavia aperea f. porcellus) and its wild ancestor, the cavy (Cavia aperea).

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

On the calculation of electrostatic interactions in proteins.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

Energetics of charge-charge interactions in proteins.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

High-resolution prediction of protein helix positions and orientations

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069153

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3715451

The inclusion of electrostatic hydration energies in molecular mechanics calculations

27 November 2018

1 reference

12 December 2020

Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes.

1 reference

12 December 2020

On the direct calculation of the free energy of quantization for molecular systems in the condensed phase

1 reference

12 December 2020

The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0069153

Identifiers

DOI

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5 March 2020

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PubMed publication ID

23874896

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