Joo Chuan Tong

Summary

Country: Singapore

Publications

  1. ncbi TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence
    Tze Hau Lam
    Laboratory of Immunogenetics and Viral Host Pathogen Genomics, Singapore Immunology Network, 8A Biomedical Grove, 03 06, Immunos, Singapore 138648
    Immunome Res 6:S6. 2010
  2. ncbi Immunological hotspots analyzed by docking simulations: evidence for a general mechanism in pemphigus vulgaris pathology and transformation
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore
    BMC Immunol 9:30. 2008
  3. ncbi Immunoinformatics: current trends and future directions
    Joo Chuan Tong
    Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis, South Tower, Singapore 138632, Singapore
    Drug Discov Today 14:684-9. 2009
  4. ncbi HLA class I restriction as a possible driving force for Chikungunya evolution
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, Fusionopolis, Singapore, Singapore
    PLoS ONE 5:e9291. 2010
  5. ncbi Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
    BMC Bioinformatics 7:S7. 2006
  6. ncbi MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Institute for Infocomm Research, Singapore
    Appl Bioinformatics 5:111-4. 2006
  7. ncbi The value of position-specific scoring matrices for assessment of protein allegenicity
    Shen Jean Lim
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
    BMC Bioinformatics 9:S21. 2008
  8. ncbi In silico grouping of peptide/HLA class I complexes using structural interaction characteristics
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore 8 Medical Drive, Singapore 117597
    Bioinformatics 23:177-83. 2007
  9. ncbi Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage
    Khar Heng Choo
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    BMC Bioinformatics 9:S15. 2008
  10. ncbi CLEVER: pipeline for designing in silico chemical libraries
    Chun Meng Song
    Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis, Singapore, Singapore
    J Mol Graph Model 27:578-83. 2009

Detail Information

Publications29

  1. ncbi TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence
    Tze Hau Lam
    Laboratory of Immunogenetics and Viral Host Pathogen Genomics, Singapore Immunology Network, 8A Biomedical Grove, 03 06, Immunos, Singapore 138648
    Immunome Res 6:S6. 2010
    ..To facilitate the usage of TAP Hunter to the scientific community, a simple, flexible and user-friendly web-server is developed and freely available at http://datam.i2r.a-star.edu.sg/taphunter/...
  2. ncbi Immunological hotspots analyzed by docking simulations: evidence for a general mechanism in pemphigus vulgaris pathology and transformation
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore
    BMC Immunol 9:30. 2008
    ..We report here a structure-based technique for the screening of DRB1*0402-specific immunological (T-cell epitope) hotspots in both Dsg3 and Dsg1 glycoproteins...
  3. ncbi Immunoinformatics: current trends and future directions
    Joo Chuan Tong
    Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis, South Tower, Singapore 138632, Singapore
    Drug Discov Today 14:684-9. 2009
    ..In this article, we review the latest trends and future directions of the field...
  4. ncbi HLA class I restriction as a possible driving force for Chikungunya evolution
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, Fusionopolis, Singapore, Singapore
    PLoS ONE 5:e9291. 2010
    ..Such an approach is useful for studying the impact of host immunity on pathogen evolution, and may help identify appropriate antigens suitable for subunit vaccine formulations...
  5. ncbi Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
    BMC Bioinformatics 7:S7. 2006
    ..We report here a structure-based model for the prediction of peptide binding to DRB1*0402 and DQB1*0503. The scoring functions were rigorously trained, tested and validated using experimentally verified peptide sequences...
  6. ncbi MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Institute for Infocomm Research, Singapore
    Appl Bioinformatics 5:111-4. 2006
    ..AVAILABILITY: The MPID-T database retrieval system is available at http://surya.bic.nus.edu.sg/mpidt CONTACT: Joo Chuan Tong (jctong@i2r.a-star.edu.sg).
  7. ncbi The value of position-specific scoring matrices for assessment of protein allegenicity
    Shen Jean Lim
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
    BMC Bioinformatics 9:S21. 2008
    ..In this study, we assessed the feasibility of using position-specific scoring matrices as a basis for predicting potential allergenicity in proteins...
  8. ncbi In silico grouping of peptide/HLA class I complexes using structural interaction characteristics
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore 8 Medical Drive, Singapore 117597
    Bioinformatics 23:177-83. 2007
    ....
  9. ncbi Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage
    Khar Heng Choo
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    BMC Bioinformatics 9:S15. 2008
    ..We report here a structure-based model for Escherichia coli DsbA 13-25 in complex with its endogenous type I SPase...
  10. ncbi CLEVER: pipeline for designing in silico chemical libraries
    Chun Meng Song
    Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis, Singapore, Singapore
    J Mol Graph Model 27:578-83. 2009
    ..The software is available at http://datam.i2r.a-star.edu.sg/clever/...
  11. ncbi AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins
    Hon Cheng Muh
    Department of Biological Sciences, National University of Singapore, Singapore
    PLoS ONE 4:e5861. 2009
    ..738), performs significantly better than a number of existing methods using an independent dataset of 1443 protein sequences. AllerHunter is available at (http://tiger.dbs.nus.edu.sg/AllerHunter)...
  12. ncbi Prediction of HLA-DQ3.2beta ligands: evidence of multiple registers in class II binding peptides
    Joo Chuan Tong
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore 8 Medical Drive, Singapore 117597, Singapore
    Bioinformatics 22:1232-8. 2006
    ..2beta peptides and illustrate that several registers exist within a candidate binding peptide. Further analysis reveals that peptides with multiple registers occur predominantly for high-affinity binders...
  13. ncbi Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, South Tower, Singapore
    Bioinformatics 25:979-80. 2009
    ..AVAILABILITY: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/...
  14. ncbi BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures
    Zeyar Aung
    Institute for Infocomm Research, A STAR Agency for Science, Technology and Research, Singapore, Singapore
    Genome Inform 21:65-76. 2008
    ..The program is available for download at: http://www1.i2r.a-star.edu.sg/~azeyar/BSAlign/...
  15. ncbi Prediction of protein allergenicity using local description of amino acid sequence
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Front Biosci 13:6072-8. 2008
    ..This approach consistently outperforms existing allergenicity prediction systems using a standardized testing dataset of experimentally validated allergens and non-allergen sequences...
  16. ncbi AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins
    Zong Hong Zhang
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Bioinformatics 23:504-6. 2007
    ..90 with 86.00% sensitivity (SE) at specificity (SP) of 86.00%. Availability: AllerTool is freely available at http://research.i2r.a-star.edu.sg/AllerTool/...
  17. ncbi Modeling the structure of bound peptide ligands to major histocompatibility complex
    Joo Chuan Tong
    Department of Biochemistry, National University of Singapore, Singapore 119260
    Protein Sci 13:2523-32. 2004
    ..In the first test, 33 out of 40 MHC class I and class II peptides and in the second test, 11 out of 15 MHC-peptide complexes were modeled with a Calpha RMSD < 1.00 A...
  18. ncbi Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)
    Tin Wee Tan
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 11:S27. 2010
    ..This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources...
  19. ncbi In silico design of small molecules
    Paul H Bernardo
    Institute of Chemical and Engineering Sciences, Agency for Science Technology and Research A STAR, Singapore, Singapore
    Methods Mol Biol 800:25-31. 2012
    ..In this chapter, we survey the most important data sources for the discovery of new molecular entities, and discuss the key considerations and guidelines for virtual chemical library design...
  20. ncbi CLEVER: A general design tool for combinatorial libraries
    Tze Hau Lam
    Data Mining Department, Institute for Infocomm Research, Singapore, Singapore
    Methods Mol Biol 685:347-56. 2011
    ..In this chapter, we describe how CLEVER is used and offer advice in interpreting the results...
  21. ncbi A multi-factor model for caspase degradome prediction
    Lawrence J K Wee
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 10:S6. 2009
    ....
  22. ncbi SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
    Lesheng Kong
    Department of Biochemistry, National University of Singapore, 8 Medical Drive, 117597, Singapore
    Nucleic Acids Res 32:W356-9. 2004
    ..Furthermore, the web service provides model stereochemical quality evaluation using PROCHECK. SDPMOD is freely accessible to academic users via the web interface at http://proline.bic.nus.edu.sg/sdpmod...
  23. ncbi Recent advances in computer-aided drug design
    Chun Meng Song
    Institute for Infocomm Research, Connexis South Tower, Singapore 138632
    Brief Bioinform 10:579-91. 2009
    ..The workflow of the entire virtual screening campaign is discussed, from data collection through to post-screening analysis...
  24. ncbi Methods and protocols for the assessment of protein allergenicity and cross-reactivity
    Joo Chuan Tong
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Front Biosci 13:4882-8. 2008
    ..This review provides an introduction to the growing literature in this area, with particular emphasis on recent developments in bioinformatics relevant to the study of allergens...
  25. ncbi Recent applications of Hidden Markov Models in computational biology
    Khar Heng Choo
    Department of Biochemistry, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
    Genomics Proteomics Bioinformatics 2:84-96. 2004
    ....
  26. ncbi Understanding infectious agents from an in silico perspective
    Joo Chuan Tong
    Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, 21 01 Connexis South Tower, Singapore 138632, Singapore
    Drug Discov Today 16:42-9. 2011
    ....
  27. ncbi A practical guide to structure-based prediction of MHC-binding peptides
    Shoba Ranganathan
    Department of Chemistry, Macquarie University, New South Wales, Australia
    Methods Mol Biol 409:301-8. 2007
    ..This chapter introduces the use of structural models as a predictive method to determine whether a peptide sequence can bind to a specific MHC allele...
  28. ncbi Methods and protocols for prediction of immunogenic epitopes
    Joo Chuan Tong
    Institute of Infocomm Research, Singapore
    Brief Bioinform 8:96-108. 2007
    ..We have also provided guidelines for predicting antigenic peptides based on the availability of existing experimental data...
  29. ncbi Functional and structural implications of the complement factor H Y402H polymorphism associated with age-related macular degeneration
    Rebecca J Ormsby
    Department of Microbiology and Infectious Diseases, Flinders Medical Centre and Flinders University of South Australia, Bedford Park, SA 5042, Australia
    Invest Ophthalmol Vis Sci 49:1763-70. 2008
    ....