NDLI: Inferring Domain–Domain Interactions From Protein

Content Provider	PubMed Central
Author	Deng, Minghua Mehta, Shipra Sun, Fengzhu Chen, Ting
Copyright Year	2002
Abstract	The interaction between proteins is one of the most important features of protein functions. Behind protein–protein interactions there are protein domains interacting physically with one another to perform the necessary functions. Therefore, understanding protein interactions at the domain level gives a global view of the protein interaction network, and possibly of protein functions. Two research groups used yeast two-hybrid assays to generate 5719 interactions between proteins of the yeast Saccharomyces cerevisiae. This allows us to study the large-scale conserved patterns of interactions between protein domains. Using evolutionarily conserved domains defined in a protein–domain database called PFAM (http://PFAM.wustl.edu), we apply a Maximum Likelihood Estimation method to infer interacting domains that are consistent with the observed protein–protein interactions. We estimate the probabilities of interactions between every pair of domains and measure the accuracies of our predictions at the protein level. Using the inferred domain–domain interactions, we predict interactions between proteins. Our predicted protein–protein interactions have a significant overlap with the protein–protein interactions (MIPS: http://mips.gfs.de) obtained by methods other than the two-hybrid assays. The mean correlation coefficient of the gene expression profiles for our predicted interaction pairs is significantly higher than that for random pairs. Our method has shown robustness in analyzing incomplete data sets and dealing with various experimental errors. We found several novel protein–protein interactions such as RPS0A interacting with APG17 and TAF40 interacting with SPT3, which are consistent with the functions of the proteins.
Related Links	http://dx.doi.org/10.1101/gr.153002
Ending Page	1548
Page Count	9
Starting Page	1540
File Format	PDF
ISSN	10889051
Journal	Genome Research
Issue Number	10
Volume Number	12
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2002-10-01
Access Restriction	Open
Rights Holder	Cold Spring Harbor Laboratory Press
Subject Keyword	Genetics(clinical) Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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

Inferring protein domain interactions from databases of interacting proteins

Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

PPIDomainMiner : Inferring domain-domain interactions from multiple sources of protein-protein interactions

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation

Inferring domain-domain interactions from protein-protein interactions.

Inferring protein domain interactions from databases of interacting proteins

Inferring chromatin-bound protein complexes from genome-wide binding assays

Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences

Monster: inferring non-covalent interactions in macromolecular structures from atomic coordinate data

Inferring Domain–Domain Interactions From Protein–Protein Interactions

Similar Documents

Inferring protein domain interactions from databases of interacting proteins

Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

PPIDomainMiner : Inferring domain-domain interactions from multiple sources of protein-protein interactions

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation

Inferring domain-domain interactions from protein-protein interactions.

Inferring protein domain interactions from databases of interacting proteins

Inferring chromatin-bound protein complexes from genome-wide binding assays

Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences

Monster: inferring non-covalent interactions in macromolecular structures from atomic coordinate data

Inferring Domain–Domain Interactions From Protein–Protein Interactions