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An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes. [PDF]
, 2018 Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification.
Campuzano, Iain DG +4 more
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Progressive search in tandem mass spectrometry
BMC Bioinformatics, 2023 Background High-throughput Proteomics has been accelerated by (tandem) mass spectrometry. However, the slow speed of mass spectra analysis prevents the analysis results from being up-to-date.
Yoonsung Joh +3 more
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Frontiers in Bioinformatics, 2023 Protein annotation errors can have significant consequences in a wide range of fields, ranging from protein structure and function prediction to biomedical research, drug discovery, and biotechnology.
Arnaud Kress +3 more
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BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data
Biology Direct, 2022 Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes ...
Markus Sutter, Cheryl A. Kerfeld
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CAPS: coevolution analysis using protein sequences [PDF]
Bioinformatics, 2006 Abstract Summary: Coevolution Analysis using Protein Sequences (CAPS) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies ...
Mario A, Fares, David, McNally
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Filtering Degenerate Patterns with Application to Protein Sequence Analysis
Algorithms, 2013 In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g., [FY ]DPC[LIM][ASG]C[ASG], are, in general, represented by ...
Matteo Comin, Davide Verzotto
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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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MethodsX, 2022 The wealth of sequence data available on public databases is increasing at an exponential rate, and while tremendous efforts are being made to make access to these resources easier, these data can be challenging for researchers to reuse because ...
Kyra Dougherty, Katalin A. Hudak
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A Receptor Component of the Chloroplast Protein Translocation Machinery [PDF]
, 1994 The chloroplast outer envelope protein OEP86 functions as a receptor in precursor protein translocation into chloroplasts. Sequence analysis suggests that the precursor of OEP86 is directed to the chloroplast outer envelope by a cleavable, negatively ...
Heemeyer, Frank +4 more
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Analysis of protein chameleon sequence characteristics [PDF]
Bioinformation, 2009 Conversion of local structural state of a protein from an alpha-helix to a beta-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized
Ghozlane, Amine +3 more
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