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14 AprVaEng

Posted by Widodo Biologi in
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UAS TEKNOLOGI VAKSIN dikerjakan secara online pada jam ujian sesuai jadwal, dengan cara login di: www.classmarker.com/register/
dengan menggunakan KODE khusus sebagai berikut: kode akses-teknologi vaksin

 

 

Supplemental Materials:

  1. Vaccine research catalog
  2. web-based tool for vaccine design
  3. Bioinformatic developing peptide-based vaccine

Open-Source Softwares and Data Bases

  1. PSORTb: PSORTb (v.2.0) is probably the most precise bacterial localization prediction tool. PSORTb is under the GNU General Public Licence (GNU GPL).
  2. TMHMM: Prediction of transmembrane helices in proteins. TMHMM is uder Academic Software License Agreement.
  3. SPAAN: Prediction of adhesins and adhesin-like proteins. According to the SPAAN publication, the SPAAN program is freely available.
  4. BLAST: NCBI sequence similarity alignment and analysis program. BLAST is a USA NCBI program within the public domain.
  5. IEDB: The Immune Epitope Database and Analysis Resource. The immune epitope data obtained from IEDB is used for training Vaxitope, our epitope prediction program.
  6. Vaxign: vaccine Design
  7. AntiJen: A database containing quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological Protein-Protein interactions.
  8. Bcipep: A database of B cell epitopes.
  9. IEDB Analysis Resource: A list of IEDB epitope prediction and anlaysis tools.
  10. JenPep: A database of quantitative binding data for immunological protein-peptide interactions.
  11. RANKPEP: A web-based computational program for prediction of binding peptides to Calss I & II MHC molecules.

 

 

 Selected Publications

  1. Rappuoli R. Reverse vaccinology. Curr Opin Microbiol. 2000 Oct;3(5):445-50. Review. PMID: 11050440.
  2. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatic. 2005 Mar 1;21(5):617-23. PMID: 15501914.
  3. Käll L, Krogh A, Sonnhammer EL. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics. 2005 Jun;21 Suppl 1:i251-7. PMID: 15961464.
  4. Sachdeva G, Kumar K, Jain P, Ramachandran S. SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks. Bioinformatics. 2005 Feb 15;21(4):483-91. PMID: 15374866.
  5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 215:403-410; 1990. PMID: 2231712.
  6. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, S choenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol. 2005 Mar;3(3):e91. PMID: 15760272.
  7. He Y, et al.  2010.Vaxign: the first web-based vaccine design program for reverse vaccinology and an application for vaccine development. Journal of Biomedicine and Biotechnology. [PMID: 20671958]
  8.      Xiang Z, He Y. 2009. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology.
  9.      He Y, Xiang Z. 2010. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.  PMID: 20875156.
  10.      McNamara L, et al. Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosis.   [PMID: 20353587]
  11. McLellan JS, et all (2011) Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9External Web Site Policy. Nature. 480(7377):336-43. Epub Nov 23.
  12. Hansman GS, et all(2011) Structural basis for norovirus inhibition and fucose mimicry by citrateExternal Web Site Policy. J Virol. 86(1):284-92. Epub Oct 26.
  13. Kong R,et all (2011) Broad and Potent Neutralizing Antibody Responses Elicited in Natural HIV-2 InfectionExternal Web Site Policy. J Virol. Epub Oct 26.
  14. Wu X, et all (2011). Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep SequencingExternal Web Site Policy. Science. 333(6049):1593-602. Epub Aug 11th
  15. Bonsignori M, et all (2011). Analysis of a Clonal Lineage of HIV-1 Envelope V2/V3 Conformational Epitope-Specific Broadly Neutralizing Antibodies and Their Inferred Unmutated Common AncestorsExternal Web Site Policy. J Virol. 85(19):9998-10009. Epub Jul 27th
  16. Kwong PD, Shapiro L. (2011). Vaccine design reaches the atomic level. Sci Transl Med.13;3(91):91ps29.
  17.  Sastry M, et all (2011). Mammalian Production of an Isotopically Enriched Outer Domain of the HIV-1 gp120 Glycoprotein for NMR SpectroscopyExternal Web Site Policy. JBNMR. 50(3), 197-207 Epub Jun 12th.
  18. Hansman GS, et all (2011). Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of VulnerabilityExternal Web Site Policy. J Virol. 85(13):6687-701. Epub Apr 27th.
  19.  Y, Zhang B, et all (2010). Crystal structure of human antibody 2909 reveals conserved features of quaternary-specific antibodies that potently neutralize HIV-1External Web Site Policy. J Virol.85(6):2524-35. Epub Dec 29th. PDB: 3piq.
  20.  Zhou T, et all (2010). Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01External Web Site Policy. Science. 329 (5993), 811-817 Epub July 8.
  21. Pancera M, et all(2010). Crystal structure of PG16 and chimeric dissection with somatically related PG9: Structure-function analysis of two quaternary-specific antibodies that effectively neutralize HIV-1External Web Site Policy. J Virol. 84, 8098-8110 Epub June 10.

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