Separated topologies--a method for relative binding free energy calculations using orientational restraints (Q36688022)

15 August 2017

Separated topologies--a method for relative binding free energy calculations using orientational restraints (English)

1 reference

15 August 2017

3

Ken A Dill

1 reference

15 August 2017

1

Gabriel J Rocklin

1 reference

15 August 2017

David L Mobley

2

1 reference

PMC publication ID

3598757

15 August 2017

language of work or name

English

0 references

publication date

1 February 2013

1 reference

Journal of Chemical Physics

15 August 2017

1 reference

15 August 2017

138

1 reference

15 August 2017

8

1 reference

15 August 2017

085104

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Perspective: Alchemical free energy calculations for drug discovery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Alchemical free energy methods for drug discovery: progress and challenges

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Statistically optimal analysis of samples from multiple equilibrium states

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Predicting absolute ligand binding free energies to a simple model site

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Automatic atom type and bond type perception in molecular mechanical calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Protein-Ligand Complexes: Computation of the Relative Free Energy of Different Scaffolds and Binding Modes.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Hit identification and binding mode predictions by rigorous free energy simulations

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

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

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3598757

Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens

5 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4792251

Multidimensional replica-exchange method for free-energy calculations

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4792251

The Development of Replica-Exchange-Based Free-Energy Methods

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4792251

21 January 2018

Identifiers

DOI

10.1063/1.4792251

1 reference

15 August 2017

1 reference

PMC publication ID

3598757

15 August 2017

PubMed publication ID

23464180

1 reference

PMC publication ID

3598757