Evidence map›Paper›PMID 33497567›Full record

ArticleThe journal of physical chemistry. B2021

GPU-Accelerated Flexible Molecular Docking.

Mengran Fan, Jian Wang, Huaipan Jiang, Yilin Feng, Mehrdad Mahdavi, Kamesh Madduri, Mahmut T Kandemir, Nikolay V Dokholyan

Abstract read
In one paragraph

Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Accelerating AutoDock Vina with GPUs.Molecules (Basel, Switzerland) · 2022
    Article
  3. 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

8 authors.

Mengran FanSchool of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
Jian WangDepartment of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States.ORCID 0000-0001-7768-2802
Huaipan JiangSchool of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
Yilin FengSchool of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
Mehrdad MahdaviSchool of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.ORCID 0000-0003-2679-6679
Kamesh MadduriSchool of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
Mahmut T KandemirSchool of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
Nikolay V DokholyanDepartment of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States.ORCID 0000-0002-8225-4025

Funding

Penn State Clinical and Translational Science InstituteUL1TR002014 · NCATS · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI KRASCHNEWSKI, JENNIFER L. · 2016 to 2025
$33.7M
Nanoscale programming of cellular and physiological phenotypes: EquipmentR35GM134864 · NIGMS · UNIVERSITY OF VIRGINIA · PI Nikolay Dokholyan · 2020 to 2026
$5.2M
Engineering allostery for in vivo protein controlR01GM123247 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DOKHOLYAN, NIKOLAY · 2017 to 2019
$1.5M
NCATS NIH HHS UL1 TR002014NIGMS NIH HHS R01 GM123247NIGMS NIH HHS R35 GM134864
6 · The paper itself

Abstract

Virtual screening is a key enabler of computational drug discovery and requires accurate and efficient structure-based molecular docking. In this work, we develop algorithms and software building blocks for molecular docking that can take advantage of graphics processing units (GPUs). Specifically, we focus on MedusaDock, a flexible protein-small molecule docking approach and platform. We accelerate the performance of the

Indexed as

AlgorithmsSoftwareComputer GraphicsLigandsMolecular Docking SimulationProteinsLigandsProteins

Identifiers

PMID33497567
PMCPMC10661840

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.