Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions (Q30386091)

21 September 2017

Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions (English)

1 reference

21 September 2017

computational biology

1 reference

2

Arieh Warshel

1 reference

21 September 2017

Nidhi Singh

1

1 reference

PMCID

2868600

21 September 2017

language of work or name

English

0 references

publication date

1 May 2010

1 reference

21 September 2017

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21 September 2017

78

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21 September 2017

7

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21 September 2017

1705-1723

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A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes

21 September 2017

1 reference

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Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Physics-based methods for studying protein-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution

20 June 2018

1 reference

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Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Modeling electrostatic effects in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta

20 June 2018

1 reference

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Virtual screening of chemical libraries

20 June 2018

1 reference

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Partition of protein solvation into group contributions from molecular dynamics simulations.

20 June 2018

1 reference

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Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

20 June 2018

1 reference

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Free energy calculations and ligand binding

20 June 2018

1 reference

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Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

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

20 June 2018

1 reference

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Free energy simulations come of age: protein-ligand recognition

20 June 2018

1 reference

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Ligand binding affinities from MD simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Dynamics of biochemical and biophysical reactions: insight from computer simulations

20 June 2018

1 reference

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Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition

20 June 2018

1 reference

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What are the dielectric "constants" of proteins and how to validate electrostatic models?

20 June 2018

1 reference

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How important are entropic contributions to enzyme catalysis?

20 June 2018

1 reference

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Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

20 June 2018

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=2868600

Remarks about protein structure precision

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Empirical potentials and functions for protein folding and binding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

The "cratic correction" and related fallacies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

On the calculation of electrostatic interactions in proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Evaluation of catalytic free energies in genetically modified proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Computational method for the design of enzymes with altered substrate specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Electrostatic Energy and Macromolecular Function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

An improved method to predict the entropy term with the MM/PBSA approach.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Predicting drug-resistant mutations of HIV protease

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Using a charging coordinate in studies of ionization induced partial unfolding

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

Charge Optimization Increases the Potency and Selectivity of a Chorismate Mutase Inhibitor

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

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.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2868600

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

26 November 2018

1 reference

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Remarks about protein structure precision. erratum

26 November 2018

1 reference

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A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding.

26 November 2018

1 reference

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Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction

26 November 2018

1 reference

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Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

26 November 2018

1 reference

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Loss of translational entropy in binding, folding, and catalysis

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Validation and use of the MM-PBSA approach for drug discovery

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Ligand binding affinity prediction by linear interaction energy methods

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Binding thermodynamics of substituted diaminopyrimidine renin inhibitors

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Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

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Thermodynamic analysis of binding of p-substituted benzamidines to trypsin

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Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin

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Avidin and streptavidin

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Absolute and relative entropies from computer simulation with applications to ligand binding

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Combinedab initioand Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution

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Synthetic Adenine Receptors: Direct Calculation of Binding Affinity and Entropy

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Identifiers

DOI

10.1002/PROT.22687

1 reference

21 September 2017

1 reference

21 September 2017

1 reference

PMCID

2868600