China
Africa
Explore chapters and articles related to this topic
An Efficient Protein Structure Prediction Using Genetic Algorithm
Published in Abdel-Badeeh M. Salem, Innovative Smart Healthcare and Bio-Medical Systems, 2020
Mohamad Yousef, Tamer Abdelkader, Khaled El-Bahnasy
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].
Molecular biology
Published in Maxine Lintern, 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.
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).
A new triple chimeric protein as a high immunogenic antigen against anthrax toxins: theoretical and experimental analyses
Published in Immunopharmacology and Immunotoxicology, 2019
Masoud Abdous, Sadegh Hasannia, Ali Hatef Salmanian, Seyed Shahryar Arab, Abbas Shali, Ghorban Ali Alizadeh, Afshin Hajizadeh, Abolfazl Khafri, Ammar Mohseni
The first structure of the ELP was evaluated using the ProtParam online software on the ExPasy tools site and EditSeq software was used to confirm the results. The secondary structure of the ELP was examined using the YASPIN online server (http://www.ibi.vu.nl/programs/yaspin). The third structure of the ELP modeled protein was determined using chimera software. The prediction of linear and spatial epitopes was done using the online tools of Bcepred (http://crdd.osdd.net/raghava/bcepred/) and Ellipro (http://tools.iedb.org/ellipro/result/predict/), respectively. Acceptable threshold of spatial epitope index score in the Ellipro software was 0.5. The ELP antigenicity was predicted by the Vaxijen v.2.0 online software (www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html). Threshold of antigenicity in this software was 0.4.
Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design
Published in Pathogens and Global Health, 2023
Chin Peng Lim, Boon Hui Kok, Hui Ting Lim, Candy Chuah, Badarulhisam Abdul Rahman, Abu Bakar Abdul Majeed, Michelle Wykes, Chiuan Herng Leow, Chiuan Yee Leow
Common parameters that are considered when selecting protein vaccine candidates include antigenicity, allergenicity and physicochemical properties. Under this category, altogether 34 different tools can be employed (Table 4). VaxiJen is a server developed for alignment-independent recognition and prediction of protective antigens of bacterial, viral and tumour origin. The server contains models derived by ACC pre-processing of amino acids properties for protein classification and quantitative structure–activity relationships (QSAR) studies of peptides with different lengths [111]. The ExPASy server contains a variety of databases and analysis tools, focusing on proteins and proteomics. On the other hand, ProtParam is an extensively-used tool that is able to compute physicochemical properties from a protein sequence, without requiring any additional information. These properties include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index, and grand average of hydropathicity index (GRAVY). The amino acid and atomic compositions are self-explanatory. The query protein can either be specified as a Swiss-Prot/TrEMBL accession number or as a raw sequence [112]. Finally, similar to VaxiJen, ACC pre-processing is applied to sets of known allergens with different origins and routes of exposure in AllerTop. From here, alignment-independent models for allergen recognition are established based on the chemical properties of amino acid sequences. A mirror set of non-allergens is compiled from the same species. Five machine learning methods including discriminant analysis by partial least squares (DA-PLS), logistic regression (LR), decision tree (DT), naïve Bayes (NB) and k nearest neighbours (kNN) are utilized for the differentiation between allergens and non-allergens. The high sensitivity is seen by the ability to identify new allergens which are structurally diverse in comparison to existing allergens [113]. Overall, these tools can be used to identify potential new vaccine candidates.