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Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases [PDF]
Cellular and Molecular Life SciencesComputational prediction of intrinsic disorder in protein sequences is an impactful and growing research area, recently infused with deep learning and protein language models, prompting the need to assess the impact of these advancements.
Kui Wang +3 more
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Protein sequence databases [PDF]
Current Opinion in Chemical Biology, 2000 A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each ...
Apweiler, Rolf +2 more
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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
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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.
C H, Wu, S, Shivakumar, H, Huang
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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
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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
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The Halophile Protein Database [PDF]
Database, 2014 Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions.
Sharma, Naveen +6 more
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The Protein Mutant Database [PDF]
Nucleic Acids Research, 1999 Currently the protein mutant database (PMD) contains over 81 000 mutants, including artificial as well as natural mutants of various proteins extracted from about 10 000 articles. We recently developed a powerful viewing and retrieving system (http://pmd.ddbj.nig.ac.jp), which is integrated with the sequence and tertiary structure databases. The system
T, Kawabata, M, Ota, K, Nishikawa
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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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SwissPalm: Protein Palmitoylation database [PDF]
F1000Research, 2015 Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from
Mathieu Blanc +6 more
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