Literature DB >> 24729746

Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer.

Sally R Ellingson1, Sivanesan Dakshanamurthy2, Milton Brown2, Jeremy C Smith3, Jerome Baudry3.   

Abstract

In this paper we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this MPI version of Autodock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.

Entities:  

Keywords:  Automated molecular docking; Drug discovery; High-performance computing; Virtual high-throughput screening

Year:  2014        PMID： 24729746      PMCID： PMC3979631          DOI： 10.1002/cpe.3070

Source DB:  PubMed          Journal:  Concurr Comput        ISSN： 1532-0626            Impact factor:   1.536


  13 in total

1.  Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach.

Authors:  Y Z Chen; C Y Ung
Journal:  J Mol Graph Model       Date:  2001       Impact factor: 2.518

Review 2.  Structural modelling and dynamics of proteins for insights into drug interactions.

Authors:  Tim Werner; Michael B Morris; Siavoush Dastmalchi; W Bret Church
Journal:  Adv Drug Deliv Rev       Date:  2011-12-01       Impact factor: 15.470

3.  Evaluation of various inverse docking schemes in multiple targets identification.

Authors:  Liu Hui-fang; Shen Qing; Zhang Jian; Fu Wei
Journal:  J Mol Graph Model       Date:  2010-09-29       Impact factor: 2.518

Review 4.  Virtual screening of chemical libraries.

Authors:  Brian K Shoichet
Journal:  Nature       Date:  2004-12-16       Impact factor: 49.962

Review 5.  Calculation of protein-ligand binding affinities.

Authors:  Michael K Gilson; Huan-Xiang Zhou
Journal:  Annu Rev Biophys Biomol Struct       Date:  2007

6.  AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

Authors:  Oleg Trott; Arthur J Olson
Journal:  J Comput Chem       Date:  2010-01-30       Impact factor: 3.376

7.  Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers.

Authors:  Barbara Collignon; Roland Schulz; Jeremy C Smith; Jerome Baudry
Journal:  J Comput Chem       Date:  2010-12-07       Impact factor: 3.376

Review 8.  Molecular dynamics simulations and drug discovery.

Authors:  Jacob D Durrant; J Andrew McCammon
Journal:  BMC Biol       Date:  2011-10-28       Impact factor: 7.431

9.  Accessible high-throughput virtual screening molecular docking software for students and educators.

Authors:  Reed B Jacob; Tim Andersen; Owen M McDougal
Journal:  PLoS Comput Biol       Date:  2012-05-31       Impact factor: 4.475

10.  Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

Authors:  Lily S Cheng; Rommie E Amaro; Dong Xu; Wilfred W Li; Peter W Arzberger; J Andrew McCammon
Journal:  J Med Chem       Date:  2008-06-18       Impact factor: 7.446
View more
  2 in total

Review 1.  Drug Metabolism in Preclinical Drug Development: A Survey of the Discovery Process, Toxicology, and Computational Tools.

Authors:  Naiem T Issa; Henri Wathieu; Abiola Ojo; Stephen W Byers; Sivanesan Dakshanamurthy
Journal:  Curr Drug Metab       Date:  2017       Impact factor: 3.731

2.  1001 Ways to run AutoDock Vina for virtual screening.

Authors:  Mohammad Mahdi Jaghoori; Boris Bleijlevens; Silvia D Olabarriaga
Journal:  J Comput Aided Mol Des       Date:  2016-02-20       Impact factor: 3.686
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.