China
Africa
Explore chapters and articles related to this topic
Disease Prediction and Drug Development
Published in Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam, Introduction to Computational Health Informatics, 2019
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam
Dynamic matching technique computes sequence-similarity based upon popular matrices such as BLOSUM (BLOcks SUbstitution Matrix) and PAM (Protein Alignment Matrix). These matrices are based upon matching of the biochemical and biophysical properties of amino-acids. The match-score is positive for amino-acids having similar properties and negative for dissimilar properties. A specific popular substitution matrix is BLOSUM62 (see Table 10.3). As shown in Tables 10.2 and 10.3, similar amino-acid such as leucine and isoleucine have a similarity-core of +2; dissimilar amino-acids such as leucine and histidine have a similarity score of −4. There are many variations of BLOSUM and PAM matrices such as BLOSUM-50, BLOSUM-62, BLOSUM-80, PAM-30 and PAM-70.
Taenia solium proteins: a beautiful kaleidoscope of pro and anti-inflammatory antigens
Published in Expert Review of Proteomics, 2020
In order to identify the protein families present in VF and ESPs, BLAST map was generated. A BLAST map represents the functional groups of protein as individual clusters. All vs. all BLAST was performed using BLOSUM62 matrix on ESPs and VF proteins individually with e-value threshold set at <0.1. Depending on the percentage identity score the edges were plotted between nodes or proteins on a scale of 0–1 in a force-directed graph by using Gephi [38]. Edges without nodes were removed for better presentation of map. In the BLAST map for VF (Figure 8) and ESPs (Figure 9) we saw clusters pertaining to different cellular processes. Both maps have cytoskeleton feature involved with mobility of parasite and Aldo-Keto reductase family (AKR) which are involved in a range of metabolic signaling reactions and Alpha-2-Macroglobulin (A2M) which are abundantly found in tapeworms and is considered as acute phase proteins; they are protease inhibitor and cytokine transporters and play role in reducing blood clotting at feeding sites of the parasite in host and hence are immunomodulatory in nature [39,40]. The VF has a glycoprotein cluster, these glycoproteins are well described for their role in diagnosis of NCC whereas ESPs has secreted antigens cluster like antigen B that help parasite in immune evasion [37].
Predicting T cell recognition of MHC class I restricted neoepitopes
Published in OncoImmunology, 2018
Zeynep Koşaloğlu-Yalçın, Manasa Lanka, Angela Frentzen, Ashmitaa Logandha Ramamoorthy Premlal, John Sidney, Kerrie Vaughan, Jason Greenbaum, Paul Robbins, Jared Gartner, Alessandro Sette, Bjoern Peters
To assess the similarity of the mutated epitopes and their non-mutated counterparts, we used a BLOSUM matrix, which is based on the frequency of amino acid substitutions observed in evolutionarily related protein sequences.71,72 A BLOSUM matrix contains log-odds scores for each of the possible substitutions of the 20 amino acids, where highly conserved amino acids have the highest scores, while non-conservative substitutions have negative scores. We used the BLOSUM62 matrix, which is generated based on protein sequence alignments of 62% identity or less. For each pair of the mutated epitope and corresponding non-mutant peptide, we calculated the similarity score as previously described. 73 Briefly, for two peptides a and b the similarity score is calculated as the BLOSUM score for a and b divided by the square root of the product of the BLOSUM scores of the two peptides aligned to themselves. This method assigns two identical peptides a similarity score of 1.
Investigation of non-CB1, non-CB2 WIN55212-2-sensitive G-protein-coupled receptors in the brains of mammals, birds, and amphibians
Published in Journal of Receptors and Signal Transduction, 2018
Chris S. Breivogel, John M. McPartland, Bhavita Parekh
Amino acid designations in Box 1 use standard single-letter abbreviations, coupled with the numbering scheme of Ballesteros and Weinstein [43]. The sequences of putative orthologs were aligned using ClustalX, with default parameters. Alignments of putative orthologs were examined for amino acid residues in Box 1. The presence or absence of each amino acid motif was visually examined, and scored with either 1 (indicating presence of a motif) or 0 (indicating non-conservative substitution or deletion of a motif). Conservative amino acid substitutions were allowed, based on the BLOSUM62 substitution matrix [44], using a cutoff value of +1. ClustalX alignments of putative orthologs were also examined for overall sequence identity.