(Q28481339)

20 October 2023

Philip C Biggin

3

Philip C

Biggin

1 reference

20 October 2023

Gregory A Ross

1

Gregory A

Ross

1 reference

22396746

Creative Commons Attribution 4.0 International

20 October 2023

language of work or name

English

0 references

publication date

2012

0 references

published in

PLOS One

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volume

7

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issue

3

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page(s)

e32036

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copyright license

start time

1 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Biostructural and pharmacological studies of bicyclic analogues of the 3-isoxazolol glutamate receptor agonist ibotenic acid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Involvement of Water in Carbohydrate−Protein Binding: Concanavalin A Revisited

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Prediction of water and metal binding sites and their affinities by using the Fold-X force field

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

19 March 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Crystallographic and calorimetric analysis of peptide binding to OppA protein

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Structure-based design of potent inhibitors of scytalone dehydratase: displacement of a water molecule from the active site

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

The Cambridge Structural Database: a quarter of a million crystal structures and rising

7 April 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

7 April 2017

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Accounting for water molecules in drug design

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

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=3291545

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

The role of water molecules in computational drug design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

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=3291545

Exploiting ordered waters in molecular docking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Role of the active-site solvent in the thermodynamics of factor Xa 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=3291545

Molecular modeling of hydration in drug design.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Application and limitations of X-ray crystallographic data in structure-based ligand and drug design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Involvement of water in carbohydrate-protein 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=3291545

Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Distributions of water around amino acid residues 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=3291545

Modelling of solvent positions around polar groups 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=3291545

HINT: a new method of empirical hydrophobic field calculation for CoMFA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure−Activity Relationship Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Role of water in molecular docking simulations of cytochrome P450 2D6.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Ligand-protein cross-docking with water molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Extracting hydration sites around proteins from explicit water simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Thermodynamics of buried water clusters at a protein-ligand binding interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Structure- and property-based design of factor Xa inhibitors: Pyrrolidin-2-ones with acyclic alanyl amides as P4 motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

AcquaAlta: a directional approach to the solvation of ligand-protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

A computational tool to optimize ligand selectivity between two similar biomacromolecular targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Classification of water molecules in protein binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Diverse, high-quality test set for the validation of protein-ligand docking performance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

A new look at the statistical model identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291545

The hydrophobic interaction is long range, decaying exponentially with distance

27 November 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032036

Understanding kinase selectivity through energetic analysis of binding site waters

21 January 2018

1 reference

12 December 2020

Ligand-protein docking with water molecules

1 reference

12 December 2020

Atomic and residue hydrophilicity in the context of folded protein structures

1 reference

12 December 2020

Thermodynamic contributions of the ordered water molecule in HIV-1 protease

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

How many water molecules can be detected by protein crystallography?

1 reference

12 December 2020

Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design

1 reference

12 December 2020

4-Anilino-6,7-dialkoxyquinoline-3-carbonitrile inhibitors of epidermal growth factor receptor kinase and their bioisosteric relationship to the 4-anilino-6,7-dialkoxyquinazoline inhibitors

1 reference

12 December 2020

A challenging system: free energy prediction for factor Xa

1 reference

12 December 2020

Docking studies on PARP-1 inhibitors: insights into the role of a binding pocket water molecule

1 reference

12 December 2020

The effect of water displacement on binding thermodynamics: concanavalin A

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0032036

Identifiers

DOI

1 reference

ADS bibcode

2012PLoSO...732036R

0 references

1 reference

1 reference

22396746

1 reference