Large protein databases reveal structural complementarity and functional locality
Nature CommunicationsRecent breakthroughs in protein structure prediction have led to a surge in high-quality 3D models, highlighting the need for efficient computational solutions. In our work, we examine the structural clusters from the AlphaFold Protein Structure Database
Paweł Szczerbiak +5 more
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THE APPLICATION OF BIOINFORMATIC METHODS FOR THE ANALYSIS OF PROTEIN TARGETS OF MICROORGANISMS PRODUCING BIOSURFACTANTS [PDF]
Biotechnologia ActaAim. The objective of this study is to identify key protein targets involved in the metabolism, regulation, and transport of biosurfactants. Target selection was based on a comprehensive analysis of biological databases and scientific literature.
Ye.B. Yanvarov +3 more
doaj +1 more source
Are We Legislating Away Our Scientific Future? The Database Debate [PDF]
, 2003 The ambiguity of the present copyright laws governing the protection of databases creates a situation where database owners, unsure of how IP laws safeguard their information, overprotect their data with oppressive licenses and technological mechanisms ...
Greenbaum, Dov
core +1 more source
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps [PDF]
, 2013 Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms.
Barillot, Emmanuel +6 more
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PDBTM: Protein Data Bank of transmembrane proteins after 8 years [PDF]
, 2012 The PDBTM database (available at http://pdbtm .enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004.
Bass +33 more
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Characterisation of FAD-family folds using a machine learning approach [PDF]
, 2002 Flavin adenine dinucleotide (FAD) and its derivatives play a crucial role in biological processes. They are major organic cofactors and electron carriers in both enzymatic activities and biochemical pathways. We have analysed the relationships between
Gilbert, D, Tan, A C, Tuson, A
core
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions [PDF]
, 2012 Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes.
Luiz A. Bovolenta +2 more
core +4 more sources
Domain fusion analysis by applying relational algebra to protein sequence and domain databases
BMC Bioinformatics, 2003 Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway.
Ikura Mitsuhiko, Truong Kevin
doaj +1 more source
Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity [PDF]
, 2007 BACKGROUND The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation.
Blaudez, D. +4 more
core +3 more sources
InterPro in 2017—beyond protein family and domain annotations
Nucleic Acids Res., 2016 InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites.
R. Finn +46 more
semanticscholar +1 more source