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
doaj +6 more sources
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
doaj +3 more sources
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
doaj +2 more sources
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
doaj +2 more sources
Analysis of Fbox substrate adapter proteins using ProteoSync, a program for projection of evolutionary conservation onto protein atomic coordinates [PDF]
Computational and Structural Biotechnology JournalThe projection of conservation onto the surface of a protein’s 3D structure is a powerful way of inferring functionally important regions. For this reason, we created ProteoSync, a Python program that semi-automates the process.
Elliot Sicheri +3 more
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
Protein sectors: statistical coupling analysis versus conservation [PDF]
, 2014 Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed "sectors".
Colwell, Lucy J. +2 more
core +8 more sources
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
A sequence embedding method for enzyme optimal condition analysis
BMC Bioinformatics, 2020 Background An enzyme activity is influenced by the external environment. It is important to have an enzyme remain high activity in a specific condition.
Xiangjun Li +5 more
doaj +1 more source