NDLI: Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

Content Provider	PubMed Central
Author	Sinha, Rohita Kundrotas, Petras J. Vakser, Ilya A.
Editor	Keskin, Ozlem
Copyright Year	2012
Abstract	The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.
Related Links	http://dx.doi.org/10.1371/journal.pone.0031349
Starting Page	31349
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	2
Volume Number	7
Language	English
Publisher	Public Library of Science
Publisher Date	2012-02-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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

The Encoding of Individual Identity in Dolphin Signature Whistles: How Much Information Is Needed?

How Much Is Too Much? Assessment of Prey Consumption by Magellanic Penguins in Patagonian Colonies

Uncovering New Pathogen–Host Protein–Protein Interactions by Pairwise Structure Similarity

Phylogenetic Profiling: How Much Input Data Is Enough?

Machine Learning: How Much Does It Tell about Protein Folding Rates?

A Decade Later, How Much of Rwanda's Musculoskeletal Impairment Is Caused by the War in 1994 and by Related Violence?

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

Towards Ligand Docking Including Explicit Interface Water Molecules

How a Spatial Arrangement of Secondary Structure Elements Is Dispersed in the Universe of Protein Folds

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

Similar Documents

The Encoding of Individual Identity in Dolphin Signature Whistles: How Much Information Is Needed?

How Much Is Too Much? Assessment of Prey Consumption by Magellanic Penguins in Patagonian Colonies

Uncovering New Pathogen–Host Protein–Protein Interactions by Pairwise Structure Similarity

Phylogenetic Profiling: How Much Input Data Is Enough?

Machine Learning: How Much Does It Tell about Protein Folding Rates?

A Decade Later, How Much of Rwanda's Musculoskeletal Impairment Is Caused by the War in 1994 and by Related Violence?

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

Towards Ligand Docking Including Explicit Interface Water Molecules

How a Spatial Arrangement of Secondary Structure Elements Is Dispersed in the Universe of Protein Folds

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?