In both chart- ing and mapping, the comparison typically involves computer matching of the experimental data with amino acid or nucleotide sequence information stored in protein and DNA databases. Clearly, the two methods complement each other. For example, where MS peptide charting would be used ...
radar-chart deviation analysisoctapeptide repeat structureAnalysis of the amino acid composition of prion protein using a newly developed program for radar-chart deviation analysis has identified an abnormality or irregularity of the N-terminal flexible domain. Aromatic amino acids Trp and His together ...
As per the scope of this report, protein sequencing is the process of determining the amino acid sequence of all or part of a protein or peptide. These techniques are helpful in the identification of proteins and characterize their post-translational modifications. The Protein Sequencing Market is...
Here, we describe development of the protein-sol web server, which was previously restricted to protein solubility prediction from amino acid sequence. Tools are presented for calculating and mapping patches of hydrophobicity and charge on the protein surface. In addition, predictions of folded state ...
where p a is the probability of an amino acid a to be in the alignment column c and p ab is the background amino acid a probability distribution computed over the entire alignment (gaps are excluded). The Relative Entropy (RE) is computed for each column c of a multiple sequence alignme...
The amino acid sequence of K. pneumoniae FepA protein with the accession number of CDO13414.1 was retrieved from the NCBI protein database (https://www.ncbi.nlm.nih.gov/protein). Class I T Epitope Prediction Class I T epitopes (CD8+ T cell-specific epitopes) of antigens are presented ...
TOPCONS2 (topcons.cbr.su.se) [59] was used to analyse the amino acid sequences of human CD81 and C. albicans Sur7 and Evp1 to predict their topology and the location of transmembrane (TM) domains. The hydrophobicity plots (light blue chart) and topology diagrams (red and blue lines) ...
The deduced amino acid sequence was determined using Vector NTI and compared by BLAST to NLL sequences in the NBCI non-redundant database [46]. Gene expression analysis RNA isolation and cDNA synthesis were performed using the Purescript RNA isolation kit (Qiagen, Germantown, MD, USA) according...
all our cross-linked amino acid pairs are localized within the same membrane-bound sub-compartment. To illustrate this, we show that the IMM-embedded proteins of the mitochondrial respiratory chain are exclusively involved in membrane-separated, sub-compartment-specific cross-links (Supplementary Fig....
we do not consider proteins fromE. coliwhere there is a non-traditional amino acid annotated in the UniProt sequence, because these can indicate pseudogenes. To ensure high-diversity, low gap alignments for inference, we removed from consideration concatenated sequence alignments with Neff/L less tha...