Results 11 to 20 of about 5,259,649 (407)
Sequence composition and environment effects on residue fluctuations in protein structures [PDF]
, 2009 The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer.
Anatoly M. Ruvinsky +2 more
core +4 more sources
Word correlation matrices for protein sequence analysis and remote homology detection
BMC Bioinformatics, 2008 Background Classification of protein sequences is a central problem in computational biology. Currently, among computational methods discriminative kernel-based approaches provide the most accurate results.
Meinicke Peter, Lingner Thomas
doaj +2 more sources
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
doaj +1 more source
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
doaj +1 more source
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
semanticscholar +1 more source
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
semanticscholar +1 more source
GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level
G3: Genes, Genomes, Genetics, 2020 One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package.
Laura G. Macías +2 more
doaj +1 more source
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
semanticscholar +1 more source
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
openaire +4 more sources
Functional annotation of creeping bentgrass protein sequences based on convolutional neural network [PDF]
BMC Plant Biol 22, 227 (2022), 2021 Background: Creeping bentgrass (Agrostis soionifera) is a perennial grass of Gramineae, belonging to cold season turfgrass, but has poor disease resistance. Up to now, little is known about the induced systemic resistance (ISR) mechanism, especially the relevant functional proteins, which is important to disease resistance of turfgrass.
arxiv +1 more source