Discerning molecular interactions: a comprehensive review on biomolecular interaction databases and network analysis tools

SK Miryala, A Anbarasu, S Ramaiah - Gene, 2018‏ - Elsevier
Computational analysis of biomolecular interaction networks is now gaining a lot of
importance to understand the functions of novel genes/proteins. Gene interaction (GI) …

Analyzing protein–protein interaction networks

GCKW Koh, P Porras, B Aranda… - Journal of proteome …, 2012‏ - ACS Publications
The advent of the “omics” era in biology research has brought new challenges and requires
the development of novel strategies to answer previously intractable questions. Molecular …

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

D Warde-Farley, SL Donaldson, O Comes… - Nucleic acids …, 2010‏ - academic.oup.com
Abstract GeneMANIA (http://www. genemania. org) is a flexible, user-friendly web interface
for generating hypotheses about gene function, analyzing gene lists and prioritizing genes …

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

D Szklarczyk, A Franceschini, M Kuhn… - Nucleic acids …, 2010‏ - academic.oup.com
An essential prerequisite for any systems-level understanding of cellular functions is to
correctly uncover and annotate all functional interactions among proteins in the cell. Toward …

[HTML][HTML] A census of human soluble protein complexes

PC Havugimana, GT Hart, T Nepusz, H Yang… - Cell, 2012‏ - cell.com
Cellular processes often depend on stable physical associations between proteins. Despite
recent progress, knowledge of the composition of human protein complexes remains limited …

MINT, the molecular interaction database: 2012 update

L Licata, L Briganti, D Peluso, L Perfetto… - Nucleic acids …, 2012‏ - academic.oup.com
Abstract The Molecular INTeraction Database (MINT, http://mint. bio. uniroma2. it/mint/) is a
public repository for protein–protein interactions (PPI) reported in peer-reviewed journals …

Reactome: a database of reactions, pathways and biological processes

D Croft, G O'kelly, G Wu, R Haw… - Nucleic acids …, 2010‏ - academic.oup.com
Abstract Reactome (http://www. reactome. org) is a collaboration among groups at the
Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University …

Pathway Commons, a web resource for biological pathway data

EG Cerami, BE Gross, E Demir… - Nucleic acids …, 2010‏ - academic.oup.com
Abstract Pathway Commons (http://www. pathwaycommons. org) is a collection of publicly
available pathway data from multiple organisms. Pathway Commons provides a web-based …

ConsensusPathDB: toward a more complete picture of cell biology

A Kamburov, K Pentchev, H Galicka… - Nucleic acids …, 2011‏ - academic.oup.com
ConsensusPathDB is a meta-database that integrates different types of functional
interactions from heterogeneous interaction data resources. Physical protein interactions …

Phospho. ELM: a database of phosphorylation sites—update 2011

H Dinkel, C Chica, A Via, CM Gould… - Nucleic acids …, 2010‏ - academic.oup.com
The Phospho. ELM resource (http://phospho. elm. eu. org) is a relational database designed
to store in vivo and in vitro phosphorylation data extracted from the scientific literature and …