Evidence map›Paper›PMID 25714358›Full record

ArticleJournal of chemical information and modeling2015

The impact of side-chain packing on protein docking refinement.

Mohammad Moghadasi, Hanieh Mirzaei, Artem Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch Paschalidis, Dima Kozakov

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of chemical information and modeling, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
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  5. Article
  6. Article
  7. Protein-ligand docking using FFT based sampling: D3R case study.Journal of computer-aided molecular design · 2018
    Article
  8. Article
  9. Article
  10. Article
  11. Focused grid-based resampling for protein docking and mapping.Journal of computational chemistry · 2016
    Article
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

7 authors.

Mohammad Moghadasi†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.
Hanieh Mirzaei†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.
Artem Mamonov†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.
Pirooz Vakili†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.
Sandor Vajda†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.
Ioannis Ch Paschalidis†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.
Dima Kozakov†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.

Funding

A MULTISTAGE APPROACH TO PROTEIN-PROTEIN DOCKINGR01GM061867 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI VAJDA, SANDOR · 2000 to 2016
$4.0M
Refinement Methods for Protein Docking based on Exploring Multi-Dimensional EnergR01GM093147 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI KOZAKOV, DMYTRO, PASCHALIDIS, IOANNIS · 2011 to 2014
$1.2M
NIGMS NIH HHS GM061867NIGMS NIH HHS GM093147NIGMS NIH HHS R01 GM061867NIGMS NIH HHS R01 GM093147
6 · The paper itself

Abstract

We study the impact of optimizing the side-chain positions in the interface region between two proteins during the process of binding. Mathematically, the problem is similar to side-chain prediction, which has been extensively explored in the process of protein structure prediction. The protein-protein docking application, however, has a number of characteristics that necessitate different algorithmic and implementation choices. In this work, we implement a distributed approximate algorithm that can be implemented on multiprocessor architectures and enables a trade-off between accuracy and running speed. We report computational results on benchmarks of enzyme-inhibitor and other types of complexes, establishing that the side-chain flexibility our algorithm introduces substantially improves the performance of docking protocols. Furthermore, we establish that the inclusion of unbound side-chain conformers in the side-chain positioning problem is critical in these performance improvements. The code is available to the community under open source license.

Indexed as

Molecular Docking SimulationAlgorithmsProteinsThermodynamicsTime FactorsProteins

Identifiers

PMID25714358
PMCPMC4734134

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.