(Q37149321)

18 August 2017

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters (English)

1 reference

18 August 2017

0 references

Gabriel J Rocklin

1

0 references

David L. Mobley

object named as

David L Mobley

series ordinal

2

0 references

Ken A. Dill

series ordinal

3

object named as

Ken A Dill

1 reference

PMC publication ID

3763860

18 August 2017

language of work or name

1 reference

1 July 2013

1 reference

Journal of Chemical Theory and Computation

18 August 2017

1 reference

18 August 2017

9

1 reference

18 August 2017

7

1 reference

18 August 2017

3072-3083

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Alchemical free energy methods for drug discovery: progress and challenges

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

The hidden energetics of ligand binding and activation in a glutamate receptor

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Predicting absolute ligand binding free energies to a simple model site

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Automatic atom type and bond type perception in molecular mechanical calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Empirical force fields for biological macromolecules: overview and issues.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Development and testing of a general amber force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Probing protein electrostatics with a synthetic fluorescent amino acid.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Electrostatics of nanosystems: application to microtubules and the ribosome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

The statistical-thermodynamic basis for computation of binding affinities: a critical review

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Molecular dynamics studies on peroxidases: a structural model for horseradish peroxidase and a substrate adduct

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Classical electrostatics in biology and chemistry

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Accurate Prediction of Noncovalent Interaction Energies with the Effective Fragment Potential Method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Limiting assumptions in molecular modeling: electrostatics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Additivity principles in biochemistry

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Novel dual-targeting benzimidazole urea inhibitors of DNA gyrase and topoisomerase IV possessing potent antibacterial activity: intelligent design and evolution through the judicious use of structure-guided design and structure-activity relationship

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

A theory for the anisotropic and inhomogeneous dielectric properties of proteins

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763860

Poisson–Boltzmann Methods for Biomolecular Electrostatics

20 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24015114

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT400315Q

1 reference

18 August 2017

1 reference

PMC publication ID

3763860

18 August 2017

PubMed publication ID

24015114

1 reference

PMC publication ID

3763860