Molecular biology
Maxine Lintern in Laboratory Skills for Science and Medicine, 2018
A range of proteomics tools are available on the ExPASY (Expert Protein Analysis System) Proteomics Server.18 This provides access to a myriad of programs for activities such as protein identification and characterisation, similarity searches, pattern and profile searches, post-translation modification prediction, topology prediction, primary structure analysis, secondary and tertiary structure analysis, sequence alignment and phylogenetic analysis.
An Efficient Protein Structure Prediction Using Genetic Algorithm
Abdel-Badeeh M. Salem in Innovative Smart Healthcare and Bio-Medical Systems, 2020
Developed by the Swiss Institute of Bioinformatics (SIB) [5], it is a web server to build protein structure models using comparative approach. It is accessible via the ExPASy web server and program Deep View [6].
Identification, characterization, and molecular phylogeny of scorpion enolase (Androctonus crassicauda and Hemiscorpius lepturus)
Published in Toxin Reviews, 2023
Elham Pondehnezhadan, Atefeh Chamani, Fatemeh Salabi, Reihaneh Soleimani
We also used ExPASy to predict the physicochemical properties of enolase protein. Based on enolase sequences obtained from transcriptome analysis of A. crassicuda and H. lepturus, the enolase was found to be a 433-amino acid protein with a polar nature, a molecular mass of ∼47 kDa, and an acidic isoelectric point. This study showed that enolase with instability index (II) <40 and estimated half-life values in the range of 30 h has high stability in scorpion species. The instability index provides an in vitro prediction of the stability of proteins in a test tube. It is estimated that a stable protein has an instability index of <40 while an unstable protein has an instability index value of >40 (Rodríguez-Ruiz et al. 2019). Moreover, proteins with an in vivo half-life of more than 16 h have been reported to be highly stable proteins (Rogers et al. 1986). Enolase protein of scorpion, predicted to have a high aliphatic index and negative GRAVY value. The high amount of aliphatic index shows the thermostability of protein over a wide temperature range (Rodríguez-Ruiz et al. 2019) and the negative values of GRAVY show the polar nature of the protein (Huang et al. 2014).
Genome-wide bioinformatics analysis of FMN, SAM-I, glmS, TPP, lysine, purine, cobalamin, and SAH riboswitches for their applications as allosteric antibacterial drug targets in human pathogenic bacteria
Published in Expert Opinion on Therapeutic Targets, 2019
Nikolet Pavlova, Robert Penchovsky
We have used databases to collect information for bioinformatics analyses of riboswitches, including GeneBank of the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/genbank), KEGG – Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/) and Protein Data Bank (PDB). We have obtained the nucleotide sequences of riboswitches in individual human pathogenic bacteria borrowed from the Rfam 12.0 database (https://rfam.sanger.ac.uk/). We have used the BioCyc database (https://biocyc.org/) and bioinformatics tools from ExPASy Bioinformatics Resource Portal (https://www.expasy.org/). The used methods are BLAST search algorithm for detection of local regions of similarity between sequences, ClustalX/ClustalW (http://www.clustal.org/clustal2/) as a multi-sequence alignment program for Windows. In addition, we apply a motif search applet at http://penchovsky.atwebpages.com/applications.php?page=43 from our Essential Bioinformatics Web Server (EBWS) [27]. We employed several bioinformatics applets from the Essential Bioinformatics Web Services (EBWS) at http://penchovsky.atwebpages.com/applications.php, including Motif Searcher (http://penchovsky.atwebpages.com/applications.php?page=43) and Prokaryotic ORF Finder (http://penchovsky.atwebpages.com/applications.php?page=45) applets.
Peptidomics and proteogenomics: background, challenges and future needs
Published in Expert Review of Proteomics, 2021
Rui Vitorino, Manisha Choudhury, Sofia Guedes, Rita Ferreira, Visith Thongboonkerd, Lakshya Sharma, Francisco Amado, Sanjeeva Srivastava
The constellation World 2D-PAGE, developed and maintained by the Swiss Institute of Bioinformatics, uses the ExPASy server for publishing two-dimensional gel electrophoresis data. The database consists of i) a list of 2-D PAGE related databases, servers, and services, ii) a dynamic portal with the ability to query worldwide gel-based proteomics databases created using the Make 2D-DB package, and iii) a public repository for gel-based proteomics data that also includes MS-based data. This database provides tools for easy use of the website, i.e. the Make 2D-DB package, the Melanie Viewer, and MIAPEGelDB.
Related Knowledge Centers
- Bioinformatics
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