AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. (Q51304233)

PubMed publication ID

27886114

3 April 2018

http://europepmc.org/abstract/MED/27886114

title

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking (English)

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13 May 2020

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Shota Uehara

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6274120&resulttype=core&format=json

13 May 2020

Shigenori Tanaka

series ordinal

2

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13 May 2020

language of work or name

English

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publication date

23 November 2016

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PubMed publication ID

27886114

3 April 2018

http://europepmc.org/abstract/MED/27886114

published in

Molecules

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13 May 2020

volume

21

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13 May 2020

issue

11

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Creative Commons Attribution 4.0 International

13 May 2020

copyright license

start time

23 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Molecular binding: Under water's influence

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Water in cavity-ligand recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Substrate specificity and affinity of a protein modulated by bound water molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Classification of water molecules in protein binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Prediction of the water content in protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Adding calorimetric data to decision making in lead discovery: a hot tip

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Replacement of water molecules in a phosphate binding site by furanoside-appended lin-benzoguanine ligands of tRNA-guanine transglycosylase (TGT)

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Impact of Surface Water Layers on Protein--Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Analysis of water patterns in protein kinase binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

WATsite: hydration site prediction program with PyMOL interface

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Structural properties of hydration shell around various conformations of simple polypeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Extracting hydration sites around proteins from explicit water simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Docking and scoring in virtual screening for drug discovery: methods and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Challenges and advances in computational docking: 2009 in review

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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/10.3390/MOLECULES21111604

Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Investigation on the effect of key water molecules on docking performance in CSARdock exercise

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Exploiting ordered waters in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

A semiempirical free energy force field with charge-based desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Rapid context-dependent ligand desolvation in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Ligand solvation in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Automated docking of substrates to proteins by simulated annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Dewetting transitions in protein cavities

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

VMD: visual molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Protein-ligand docking using fitness learning-based artificial bee colony with proximity stimuli

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

SODOCK: swarm optimization for highly flexible protein-ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Electrostatic effects in proteins: comparison of dielectric and charge models

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Investigation of MM-PBSA rescoring of docking poses

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Incorporating replacement free energy of binding-site waters in molecular docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Preparation, characterization, and the crystal structure of the inhibitor ZK-807834 (CI-1031) complexed with factor Xa

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

PDB-wide collection of binding data: current status of the PDBbind database

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Consideration of molecular weight during compound selection in virtual target-based database screening

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Assessment of programs for ligand binding affinity prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

The discovery and development of rivaroxaban, an oral, direct factor Xa inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Perspectives on factor Xa inhibition

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous properly of water

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Enthalpy-Entropy Compensation upon Molecular Conformational Changes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Nicotinic pharmacophore: the pyridine N of nicotine and carbonyl of acetylcholine hydrogen bond across a subunit interface to a backbone NH.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/MOLECULES21111604

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

21 January 2018

1 reference

12 December 2020

Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4

1 reference

12 December 2020

Computing the Thermodynamic Contributions of Interfacial Water

1 reference

12 December 2020

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

1 reference

12 December 2020

WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking

1 reference

12 December 2020

Biomolecular energy calculations using transputer technology

1 reference

12 December 2020

Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions

1 reference

12 December 2020

10.3390/MOLECULES21111604

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6274120&resulttype=core&format=json

release_cle3mpptnrcchjtddh3p45kt4a

13 May 2020

Fatcat ID

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Fatcat

https://api.fatcat.wiki/v0/release/cle3mpptnrcchjtddh3p45kt4a

24 November 2022

mapped directly with Wikidata item

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6274120&resulttype=core&format=json

13 May 2020

PubMed publication ID

27886114

1 reference