PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements (Q42182002)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21214225%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements (English)

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19 January 2020

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2

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19 January 2020

author name string

Yat T Tang

series ordinal

1

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19 January 2020

publication date

7 January 2011

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Journal of Chemical Information and Modeling

19 January 2020

published in

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19 January 2020

volume

51

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19 January 2020

issue

2

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19 January 2020

page(s)

214-228

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Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding

19 January 2020

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26 October 2017

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26 October 2017

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Compensating enthalpic and entropic changes hinder binding affinity optimization

26 October 2017

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

26 October 2017

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A critical assessment of docking programs and scoring functions

26 October 2017

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The PDBbind database: methodologies and updates

26 October 2017

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Virtual screening of chemical libraries

26 October 2017

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

26 October 2017

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The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

26 October 2017

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The ABRF-MIRG'02 study: assembly state, thermodynamic, and kinetic analysis of an enzyme/inhibitor interaction

26 October 2017

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Structure-based virtual screening: an overview

26 October 2017

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Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

26 October 2017

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

26 October 2017

1 reference

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Principles of docking: An overview of search algorithms and a guide to scoring functions

26 October 2017

1 reference

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Detailed analysis of scoring functions for virtual screening

26 October 2017

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Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

26 October 2017

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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

26 October 2017

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Development and validation of a genetic algorithm for flexible docking

26 October 2017

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Computational methods to predict binding free energy in ligand-receptor complexes

26 October 2017

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

26 October 2017

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26 October 2017

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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

26 October 2017

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

29 May 2018

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29 May 2018

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17 August 2018

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17 August 2018

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17 August 2018

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Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking.

17 August 2018

1 reference

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New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy.

17 August 2018

1 reference

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An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.

17 August 2018

1 reference

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Assessing scoring functions for protein-ligand interactions

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3046228

Comparative evaluation of 11 scoring functions for molecular docking

17 August 2018

1 reference

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Rearrangement of Cruickshank's formulae for the diffraction-component precision index.

17 August 2018

1 reference

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Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3046228

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

17 August 2018

1 reference

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Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

17 August 2018

1 reference

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

17 August 2018

1 reference

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The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

30 September 2018

1 reference

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Free R value: cross-validation in crystallography

30 September 2018

1 reference

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Ligand binding affinity prediction by linear interaction energy methods

3 November 2018

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12 December 2020

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions

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12 December 2020

LigScore: a novel scoring function for predicting binding affinities

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12 December 2020

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

12 December 2020

Identifiers

DOI

10.1021/CI100257S

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21214225%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

DBLP publication ID

journals/jcisd/TangM11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21214225%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

21214225

1 reference