(Q35751099)

10 August 2017

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

1 reference

10 August 2017

1 reference

Lingle Wang

1

1 reference

10 August 2017

B J Berne

series ordinal

2

1 reference

10 August 2017

Richard A Friesner

series ordinal

3

1 reference

10 August 2017

language of work or name

English

0 references

publication date

23 January 2012

1 reference

Proceedings of the National Academy of Sciences of the United States of America

10 August 2017

1 reference

10 August 2017

109

1 reference

10 August 2017

6

1 reference

10 August 2017

1937-1942

1 reference

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

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Alchemical free energy methods for drug discovery: progress and challenges

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Advances in all atom sampling methods for modeling protein-ligand binding affinities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Ligand binding to protein-binding pockets with wet and dry regions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Efficient drug lead discovery and optimization

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Novel procedure for modeling ligand/receptor induced fit effects.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Development and testing of a general amber force field

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Thrombin signalling and protease-activated receptors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277581

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

25 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1114017109

Improved Replica Exchange Method for Native-State Protein Sampling

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22308365

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22308365

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Design of novel, potent, noncovalent inhibitors of thrombin with nonbasic P-1 substructures: rapid structure-activity studies by solid-phase synthesis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22308365

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1114017109

1 reference

10 August 2017

0 references

1 reference

10 August 2017

1 reference