MESSA: MEta-Server for protein Sequence Analysis [PDF]
BMC Biology, 2012 Background Computational sequence analysis, that is, prediction of local sequence properties, homologs, spatial structure and function from the sequence of a protein, offers an efficient way to obtain needed information about proteins under study.
Cong Qian, Grishin Nick V
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iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization. [PDF]
Nucleic Acids Res, 2021 Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins.
Chen Z +11 more
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Analysis of the Sequence Characteristics of Antifreeze Protein [PDF]
Life, 2021 Antifreeze protein (AFP) is a proteinaceous compound with improved antifreeze ability and binding ability to ice to prevent its growth. As a surface-active material, a small number of AFPs have a tremendous influence on the growth of ice.
Yu-Hang Zhang +7 more
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Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis [PDF]
iScience, 2021 Summary: Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations
Keisuke Motone +2 more
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Protein sequence analysis in the context of drug repurposing [PDF]
BMC Medical Informatics and Decision MakingMotivation Drug repurposing speeds up the development of new treatments, being less costly, risky, and time consuming than de novo drug discovery. There are numerous biological elements that contribute to the development of diseases and, as a result, to ...
Natalia García Sánchez +3 more
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Interactive Analysis of Functional Residues in Protein Families
mSystems, 2022 A protein’s function depends on functional residues that determine its binding specificity or its catalytic activity, but these residues are typically not considered when annotating a protein’s function.
Morgan N. Price, Adam P. Arkin
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Evolutionary Study of Protein Short Tandem Repeats in Protein Families
Biomolecules, 2023 Tandem repeats in proteins are patterns of residues repeated directly adjacent to each other. The evolution of these repeats can be assessed by using groups of homologous sequences, which can help pointing to events of unit duplication or deletion.
Pablo Mier, Miguel A. Andrade-Navarro
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ProteinBERT: a universal deep-learning model of protein sequence and function
bioRxiv, 2021 Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis.
N. Brandes +4 more
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Protein Sequence Analysis Using the MPI Bioinformatics Toolkit
Current Protocols in Bioinformatics, 2020 The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) provides interactive access to a wide range of the best‐performing bioinformatics tools and databases, including the state‐of‐the‐art protein sequence comparison methods HHblits and HHpred.
Felix Gabler +7 more
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Representation learning applications in biological sequence analysis
bioRxiv, 2021 Remarkable advances in high-throughput sequencing have resulted in rapid data accumulation, and analyzing biological (DNA/RNA/protein) sequences to discover new insights in biology has become more critical and challenging.
Hitoshi Iuchi +8 more
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