NDLI: Parallel Protein Docking Tool

Content Provider	IEEE Xplore Digital Library
Author	Sović, I. Antulov-Fantulin, N. Čanadi, I. Piškorec, M. Šikić, M.
Copyright Year	2010
Description	Author affiliation: Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, 10000, Croatia (Sović, I.; Antulov-Fantulin, N.; Čanadi, I.; Piškorec, M.; Šikić, M.)
Abstract	Parallel Protein Docking Tool (PPDT) system is performing a shape based process of protein docking using spherical harmonics. The software is made from scratch in C++. Input data are two PDB (Protein Data Bank) files and desired docking parameters. The PDB files hold information about protein's atom coordinates in three dimensional space. Protein structures are transformed with spherical functions which allow fast rotation and translation of 3D shapes in space. By translation and rotation (with a given resolution of angles and distance) the surface complementarity is tested for each orientation of two proteins in 3D space. The orientations are then ranked according to the given scores. The output PDB file now holds orientations with best scores ready for visualization. As a part of the system a tool for visualization of molecules was developed. It's purpose is to provide a visualization of molecular structure in all phases of protein docking process. The visualizer also allows interactive translation and rotation of input proteins and evaluation of their complementarity in real time. Although docking tools that use spherical harmonics already exist, we implemented a parallel version using MPI (message passing interface). In this implementation any worker MPI process independently makes docking search on six dimensional subspace determined by parameters in its task. PPDT has high scalability, modularity, variable granularity of tasks and provides significant speedup comparing to a non-parallel version of software.
Starting Page	1333
Ending Page	1338
File Size	218821
Page Count	6
File Format	PDF
ISBN	9781424477630
e-ISBN	9789532330502
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-05-24
Publisher Place	Croatia
Access Restriction	Subscribed
Rights Holder	MIPRO
Subject Keyword	Visualization Protein engineering Shape Scalability Spherical harmonics MPI PDB Concurrent computing Geometry Message passing Performance analysis Protein docking Electrostatics Testing
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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