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Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. A semi-empirical method which makes use of physicochemical properties of amino acid residues and their frequencies of occurrence(More)
Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is an important human pathogen. The envelope glycoprotein (Egp), a major structural antigen, is responsible for viral haemagglutination and eliciting neutralising antibodies. The three-dimensional structure of the Egp of JEV was predicted using the knowledge-based homology modeling approach and(More)
Crystal structure data of globular proteins were used to prepare (phi, psi) probability maps of 20 proteinous amino acids. These maps were compared grid-wise with each other and a conformational similarity index was calculated for each pair of amino acids. A weight matrix, called Conformational Similarity Weight (CSW) matrix, was prepared using the(More)
Transformed B cells making monoclonal IgM-lambda anti-PR3 antibody WGH1 from a patient with Wegener's granulomatosis were used to prepare mRNA and synthesize cDNA. PCR primers for human micro and lambda chains were then employed to amplify heavy- and light-chain V-regions followed by cloning into pCR2-1 vector and sequencing. Molecular modeling of VH(More)
The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi),(More)
Helper T (Th) cell antigenic sites were predicted from the primary amino acid sequence (approximately 500 in length) of the envelope (E) glycoprotein (gp) of Japanese encephalitis (JE), West Nile (WN) and Dengue (DEN) I-IV flaviviruses. Prediction of Th epitopes was done by analyzing the occurrence of amphipathic segments, Rothbard-Taylor tetra/pentamer(More)
A simple algorithm has been developed to detect beta-bends and 'loops'-chain reversals containing five amino acid residues, using only coordinates of C alpha-atoms from crystal structure data of globular proteins using the above algorithm. Analysis of bends have showed that the total number of bends in each protein (TB) is linearly related to total number(More)
Polyclonal or monoclonal human IgM rheumatoid factors (RF) react with eight antigenic sites on the CH3 IgG domain, four sites on CH2 and two on human beta 2-microglobulin. All 14 of these RF-reactive epitopes are linear 7-11 amino acid peptides with different primary sequence. We questioned whether RF reactivity with such a variety of epitopes showing no(More)