HLAV3D

      HLA 3D is a platform for online analysis of sequence variability of HLA molecules. The website shows the sequence alignments of the antigen presenting platform of HLA I and II molecules (A1A2 and A1B1 domains, perspective) from which the variability analyses were performed. And it can also visualize the mapping of HLA sequence variability and its related 3D structure.

To use the HLAV3D and get more information, please click here.

PVS

      PVS(Protein Variability Server) is an online analysis tool that uses several variability metrics to calculate sequence variability within multiple sequence alignments.And it can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure. The files it needs include protein sequences and PDB files. Visitors can choose one of Shannon, Simpson and Wu Kabat to calculate sequence variability.

To use the PVS and get more information, please click here.

Citation:

Shannon, C. E. (1948). The mathematical theory of communication. The Bell System Technical Journal 27, 379-423, 623-656.

Reinherz, E. L. & Schlossman, S. F. (1980). The differentiation and function of human T lymphocytes: A review. Cell 19, 821-827.

Stern, L. J. & Wiley, D. C. (1994).. Antigen peptide binding by class I and class II histocompatibility proteins. Structure 2, 245-251

Madden, D. R. (1995). The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13, 587-622.

Schneider, T. D. (1997). Information content of individual genetic sequences. J Theor Biol 189, 427-441.

Garcia, K. C., Teyton, L. & Wilson, I. A. (1999). Structural basis of T cell recognition. Annu Rev Immunol 17, 369-397.

Reche P.A. & Reinherz E.L. (2003). Co-evolution of allelic variability in HLA polymorphism and T cell receptor-based immunorecognition (Submmited)

Diez-Rivero CM & Reche PA. (2009). Discovery of conserved epitopes through sequence variability analysis. Bioinformatics for immunomics; Series: Immunomics Reviews: Vol. 3. Pg. 95-101. Eds. Flower, Darren D.R.; Davies, Matthew; Ranganathan, Shoba. ISBN: 978-1-4419-0539-0.

Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, Reche PA (2008) PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res., 36:W35-41.