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Integrated web visualizations for protein-protein interaction databases [PDF]
BMC Bioinformatics, 2015 BACKGROUND: Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions.
Holzinger, Andreas +2 more
core +4 more sources
Mining Protein Databases using Machine Learning Techniques
Journal of Integrative Bioinformatics, 2008 With a large amount of information relating to proteins accumulating in databases widely available online, it is of interest to apply machine learning techniques that, by extracting underlying statistical regularities in the data, make predictions about ...
Camargo Renata da Silva +1 more
doaj +2 more sources
Nucleic Acids Res., 2022 Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scattered across ...
Damian Szklarczyk +12 more
semanticscholar +1 more source
The Landscape of Virus-Host Protein–Protein Interaction Databases
Frontiers in Microbiology, 2022 Knowledge of virus-host interactomes has advanced exponentially in the last decade by the use of high-throughput screening technologies to obtain a more comprehensive landscape of virus-host protein–protein interactions.
Gabriel Valiente
doaj +1 more source
ColabFold: making protein folding accessible to all
Nature Methods, 2022 ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold.
M. Mirdita +2 more
semanticscholar +1 more source
Closing the circle : current state and perspectives of circular RNA databases [PDF]
, 2021 Circular RNAs (circRNAs) are covalently closed RNA molecules that have been linked to various diseases, including cancer. However, a precise function and working mechanism are lacking for the larger majority.
Vandesompele, Jo +2 more
core +1 more source
Fast and accurate protein structure search with Foldseek
bioRxiv, 2022 Foldseek speeds up protein structural search by four to five orders of magnitude. As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck.
Michel van Kempen +7 more
semanticscholar +1 more source
Nucleic Acids Res., 2020 Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are particularly important due to their versatility, specificity and adaptability.
Damian Szklarczyk +11 more
semanticscholar +1 more source
Virus Pop—Expanding Viral Databases by Protein Sequence Simulation
Viruses, 2023 The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived
Julia Kende +6 more
doaj +1 more source
PS4: a next-generation dataset for protein single-sequence secondary structure prediction
BioTechniques, 2023 Protein secondary structure prediction is a subproblem of protein folding. A light-weight algorithm capable of accurately predicting secondary structure from only the protein residue sequence could provide useful input for tertiary structure prediction ...
Omar Peracha
doaj +1 more source