Results 21 to 30 of about 1,894,988 (266)
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting
Entropy, 2019 Extracting structural information from sequence co-variation has become a common computational biology practice in the recent years, mainly due to the availability of large sequence alignments of protein families.
Duccio Malinverni, Alessandro Barducci
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iSeqSearch: incremental protein search for iBlast/iMMSeqs2/iDiamond [PDF]
PeerJBackground The advancement of sequencing technology has led to a rapid increase in the amount of DNA and protein sequence data; consequently, the size of genomic and proteomic databases is constantly growing.
Hyunwoo Yoo +5 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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SeqCP: A sequence-based algorithm for searching circularly permuted proteins
Computational and Structural Biotechnology Journal, 2023 Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence.
Chi-Chun Chen +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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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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BMC Bioinformatics, 2021 Background The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources.
Elena Tea Russo +2 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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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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