Results 11 to 20 of about 516,773 (266)

Protein-protein interaction databases: keeping up with growing interactomes

Human Genomics, 2009
Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction
Lehne Benjamin, Schlitt Thomas
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ProClass protein family database [PDF]

Nucleic Acids Research, 1999
ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins.
Cathy H. Wu, Sailaja Shivakumar, Hongzhan Huang   +2 more
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Current successes and remaining challenges in protein function prediction

Frontiers in Bioinformatics, 2023
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes.
Constance J. Jeffery
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Gene and protein nomenclature in public databases

BMC Bioinformatics, 2006
Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of ...
Zimmer Ralf, Fundel Katrin
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Pfam: the protein families database [PDF]

Nucleic Acids Research, 2013
(Uploaded by Plazi for the Bat Literature Project) Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described.
Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta   +12 more
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Database of Structural Motifs in Proteins [PDF]

Bioinformatics, 2000
Abstract Summary: The database of structural motifs in proteins (DSMP) contains data relevant to helices, β-turns, γ-turns, β-hairpins, ψ-loops, β-α-β motifs, β-sheets, β-strands and disulphide bridges extracted from all proteins in the Protein Data Bank primarily using the PROMOTIF program and implemented as a web-based network service ...
Kunchur Guruprasad, Maheshuni S. Prasad, Gundu R. Kumar   +2 more
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Context-specific interactions in literature-curated protein interaction databases

BMC Genomics, 2018
Background Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates.
R. Greg Stacey, Michael A. Skinnider, Jenny H. L. Chik, Leonard J. Foster   +3 more
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How Far Are We from the Completion of the Human Protein Interactome Reconstruction?

Biomolecules, 2022
After more than fifteen years from the first high-throughput experiments for human protein–protein interaction (PPI) detection, we are still wondering how close the completion of the genome-scale human PPI network reconstruction is, what needs to be ...
Georgios N. Dimitrakopoulos, Maria I. Klapa, Nicholas K. Moschonas   +2 more
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Characterization of Protein Complexes and Subcomplexes in Protein-Protein Interaction Databases

Biochemistry Research International, 2015
The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions.
Nazar Zaki, Elfadil A. Mohamed, Antonio Mora   +2 more
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Evaluating deterministic motif significance measures in protein databases

Algorithms for Molecular Biology, 2007
Background Assessing the outcome of motif mining algorithms is an essential task, as the number of reported motifs can be very large. Significance measures play a central role in automatically ranking those motifs, and therefore alleviating the analysis ...
Azevedo Paulo J, Ferreira Pedro
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