(Q41451646)

30 September 2017

Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations (English)

1 reference

30 September 2017

2

1 reference

30 September 2017

E Prabhu Raman

1

1 reference

PMCID

3490637

30 September 2017

Alexander D Mackerell

series ordinal

3

1 reference

30 September 2017

26 March 2012

1 reference

Journal of Chemical Theory and Computation

30 September 2017

1 reference

30 September 2017

8

1 reference

30 September 2017

10

1 reference

30 September 2017

3513-3525

1 reference

Hydrophobic Binding Hot Spots of Bcl-xL Protein-Protein Interfaces by Cosolvent Molecular Dynamics Simulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

All-atom empirical potential for molecular modeling and dynamics studies of 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=3490637

The rise of fragment-based 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=3490637

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Full protein flexibility is essential for proper hot-spot mapping.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Library screening by fragment-based docking

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Computational fragment-based binding site identification by ligand competitive saturation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

CHARMM: the biomolecular simulation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Additivity in the analysis and design of HIV protease inhibitors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Fragment-based de novo ligand design by multiobjective evolutionary optimization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Free energies of ligand binding for structurally diverse compounds

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Canonical dynamics: Equilibrium phase-space distributions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Design and synthesis of a series of potent and orally bioavailable noncovalent thrombin inhibitors that utilize nonbasic groups in the P1 position

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Exhaustive docking of molecular fragments with electrostatic solvation.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Fragment-based computation of binding free energies by systematic sampling.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Fragment-Based Drug Discovery

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

A MATHEMATICAL CONTRIBUTION TO STRUCTURE-ACTIVITY STUDIES.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Functionality maps of binding sites: a multiple copy simultaneous search method

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3490637

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23144598

12 December 2020

inferred from PubMed ID database lookup

Diverse fragment clustering and water exclusion identify protein hot spots

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23144598

12 December 2020

inferred from PubMed ID database lookup

Refinement of protein conformations using a macromolecular energy minimization procedure

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23144598

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1021/CT300088R

1 reference

release_s5usbfmptbda5jgfvzwzigorda

30 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/s5usbfmptbda5jgfvzwzigorda

24 November 2022

mapped directly with Wikidata item

PMCID

3490637

1 reference

30 September 2017

1 reference

PMCID

3490637