NDLI: Refining multimeric protein complexes using conservation, electrostatics and probabilistic selection

Content Provider	IEEE Xplore Digital Library
Author	Akbal-Delibas, B. Haspel, N.
Copyright Year	2012
Description	Author affiliation: Department of Computer Science, UMass Boston, Boston, MA 02125 USA (Akbal-Delibas, B.; Haspel, N.)
Abstract	We introduce a multimeric docking refinement method that uses a scoring function based on a tight coupling between evolutionary conservation, geometry and pairwise interactions. Detection of protein complexes and their structures is crucial for understanding the role of protein complexes in the basic biology of organisms. Computational methods can provide researchers with a good starting point for the analysis of protein complexes. However, computational docking methods are often not accurate and their results need to be further refined to improve interface packing. Additionally, most docking methods focus on dimers due to the exponential growth in computational complexity caused by the addition of monomeric units. Multimeric docking and refinement methods should employ efficient selection criteria to reduce the search space. The incorporation of evolutionary conservation allows us to bias our results towards possible functional interface. We combine our search with a probabilistic selection scheme that allows us to escape local energy minima. Our results suggest that our refinement scheme can efficiently handle complexes with more than 2 monomers and help biasing the results towards complexes with native interactions, filtering out false positive results. We produce structures with better IRMSDs with respect to the known complexes and lower energies than those initial docked structures.
Starting Page	648
Ending Page	653
File Size	2980476
Page Count	6
File Format	PDF
ISBN	9781467327466
e-ISBN	9781467327473
e-ISBN	9781467327442
DOI	10.1109/BIBMW.2012.6470272
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Geometry Protein engineering Correlation Evolutionary traces Docking refinement Probabilistic logic Probability distribution Electrostatic energy Protein docking Electrostatics Multimeric complexes
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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