Evidence map›Paper›PMID 27696242›Full record

ArticleJournal of computer-aided molecular design2017

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Florentina Tofoleanu, Juyong Lee, Frank C Pickard Iv, Gerhard König, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R Brooks

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Evaluating the Performance of a Non-Bonded CuInternational journal of molecular sciences · 2020
    Article
  2. Article
  3. Article
  4. Overview of the SAMPL6 host-guest binding affinity prediction challenge.Journal of computer-aided molecular design · 2018
    Article
  5. Article
  6. Article
  7. Overview of the SAMPL5 host-guest challenge: Are we doing better?Journal of computer-aided molecular design · 2017
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Florentina TofoleanuLaboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA. florentina.tofoleanu@nih.gov.ORCID 0000-0002-2236-0512
Juyong LeeLaboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA.
Frank C Pickard IvLaboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA.
Gerhard KönigMax-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
Jing HuangLaboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA.
Minkyung BaekDepartment of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
Chaok SeokDepartment of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
Bernard R BrooksLaboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA.

Funding

Molecular Dynamics Simulations Of Biological MacromoleculesZIAHL001050 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI BROOKS, BERNARD R · 2009 to 2025
$12.9M
Intramural NIH HHS Z99 HL999999
6 · The paper itself

Abstract

As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol

Indexed as

LigandsMolecular Dynamics SimulationThermodynamicsBinding SitesMolecular ConformationMolecular StructureProtein BindingProteinsQuantum TheorySoftwareSolventsLigandsProteinsSolventsBennett acceptance ratioBinding free energy simulationsDouble decoupling methodGalaxyDock-HGHamiltonian replica exchangeMolecular dynamics simulationsThermodynamic integration

Identifiers

PMID27696242
PMCPMC6472255

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.