Darren R Flower

Summary

Affiliation: Edward Jenner Institute for Vaccine Research
Country: UK

Publications

  1. doi request reprint Using databases and data mining in vaccinology
    Matthew N Davies
    The Jenner Institute, University of Oxford, Compton, Berkshire, RG20 7NN, UK
    Expert Opin Drug Discov 2:19-35. 2007
  2. pmc AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data
    Christopher P Toseland
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, RG20 7NN, UK
    Immunome Res 1:4. 2005
  3. pmc VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
    Irini A Doytchinova
    Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St, 1000 Sofia, Bulgaria
    BMC Bioinformatics 8:4. 2007
  4. pmc Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
    Wen Liu
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 7:182. 2006
  5. pmc SVRMHC prediction server for MHC-binding peptides
    Ji Wan
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 7:463. 2006
  6. ncbi request reprint Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire, RG20 7NN, UK
    Semin Cell Dev Biol 15:693-701. 2004
  7. ncbi request reprint Databases and data mining for computational vaccinology
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
    Curr Opin Drug Discov Devel 6:396-400. 2003
  8. ncbi request reprint YBF 2004: welcome to the future
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    Drug Discov Today 10:172-3. 2005
  9. ncbi request reprint Towards in silico prediction of immunogenic epitopes
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, RG20 7NN, Berkshire, UK
    Trends Immunol 24:667-74. 2003
  10. ncbi request reprint Experimentally determined lipocalin structures
    D R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire RG20 7NN, UK
    Biochim Biophys Acta 1482:46-56. 2000

Collaborators

Detail Information

Publications83

  1. doi request reprint Using databases and data mining in vaccinology
    Matthew N Davies
    The Jenner Institute, University of Oxford, Compton, Berkshire, RG20 7NN, UK
    Expert Opin Drug Discov 2:19-35. 2007
    ..With special reference to epitope data, the authors discuss the strengths and weaknesses of the available techniques and how they can aid computer-aided vaccine design deliver added value for vaccinology...
  2. pmc AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data
    Christopher P Toseland
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, RG20 7NN, UK
    Immunome Res 1:4. 2005
    ..The database is accessible from the URL: http://www.jenner.ac.uk/antijen...
  3. pmc VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
    Irini A Doytchinova
    Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St, 1000 Sofia, Bulgaria
    BMC Bioinformatics 8:4. 2007
    ....
  4. pmc Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
    Wen Liu
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 7:182. 2006
    ....
  5. pmc SVRMHC prediction server for MHC-binding peptides
    Ji Wan
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 7:463. 2006
    ..Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort...
  6. ncbi request reprint Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire, RG20 7NN, UK
    Semin Cell Dev Biol 15:693-701. 2004
    ..Many GPCRs remain orphan receptors with no identified ligand, yet as computer-driven functional genomics starts to elaborate their functions, a new understanding of their roles in cell and developmental biology will follow...
  7. ncbi request reprint Databases and data mining for computational vaccinology
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
    Curr Opin Drug Discov Devel 6:396-400. 2003
    ..Databases and data mining, the two principal weapons at the disposal of the in silico vaccinologist, will be presented in the light of current developments...
  8. ncbi request reprint YBF 2004: welcome to the future
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    Drug Discov Today 10:172-3. 2005
  9. ncbi request reprint Towards in silico prediction of immunogenic epitopes
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, RG20 7NN, Berkshire, UK
    Trends Immunol 24:667-74. 2003
    ..Two encouraging developments - data driven artificial intelligence sequence-based methods for epitope prediction and molecular modeling methods based on three-dimensional protein structures - offer hope for the future...
  10. ncbi request reprint Experimentally determined lipocalin structures
    D R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire RG20 7NN, UK
    Biochim Biophys Acta 1482:46-56. 2000
    ..The number of solved lipocalin structures is steadily increasing, and with it increases our knowledge of this enigmatic and challenging protein family...
  11. ncbi request reprint Immunoinformatics and the prediction of immunogenicity
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, UK
    Appl Bioinformatics 1:167-76. 2002
    ....
  12. doi request reprint Advances in predicting and manipulating the immunogenicity of biotherapeutics and vaccines
    Darren R Flower
    The Jenner Institute, University of Oxford, Compton, Newbury, Berkshire, UK
    BioDrugs 23:231-40. 2009
    ..Currently, many unresolved issues must be addressed and thus circumvented before effective prediction can become routine...
  13. ncbi request reprint Beyond the superfamily: the lipocalin receptors
    D R Flower
    The Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire RG20 7NN, UK
    Biochim Biophys Acta 1482:327-36. 2000
    ..The properties of these receptors are summarized and discussed...
  14. ncbi request reprint DISSIM: a program for the analysis of chemical diversity
    D R Flower
    Department of Physical and Metabolic Sciences, Astra Charnwood, Loughborough, Leicestershire, UK
    J Mol Graph Model 16:239-53, 264. 1998
    ..The specific application of these techniques to the comparative analysis of topological indices and their use in the area of chemical diversity analysis and compound selection are also described...
  15. ncbi request reprint The lipocalin protein family: structural and sequence overview
    D R Flower
    The Edward Jenner Institute for Vaccine Research, Newbury, Berkshire, UK
    Biochim Biophys Acta 1482:9-24. 2000
    ..The superfamily is characterised by a similar structure (a repeated +1 topology beta-barrel) and by the conservation of a remarkable structural signature...
  16. ncbi request reprint Rotational superposition: a review of methods
    D R Flower
    Edward Jenner Institute for Vaccine Research, Newbury, Berkshire, UK
    J Mol Graph Model 17:238-44. 1999
    ..Thus, quaternion parameterization-based methods are the best choice for rotational superposition applications...
  17. ncbi request reprint MHCPred 2.0: an updated quantitative T-cell epitope prediction server
    Pingping Guan
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, UK
    Appl Bioinformatics 5:55-61. 2006
    ..A tool for the design of heteroclitic peptides is also included within the server. To refine the veracity of binding affinities prediction, a confidence percentage is also now calculated for each peptide predicted...
  18. ncbi request reprint Quantitative online prediction of peptide binding to the major histocompatibility complex
    Channa K Hattotuwagama
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    J Mol Graph Model 22:195-207. 2004
    ..We call this server MHCPred. Access to the server is freely available from the URL: http://www.jenner.ac.uk/MHCPred. We have exemplified our method with a model for peptides binding to the common human MHC molecule HLA-B*3501...
  19. ncbi request reprint Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships
    Channa K Hattotuwagama
    The Jenner Institute, University of Oxford, Berkshire, UK
    Methods Mol Biol 409:227-45. 2007
    ..The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred...
  20. ncbi request reprint MHCPred: bringing a quantitative dimension to the online prediction of MHC binding
    Pingping Guan
    Edward Jenner Institute for Vaccine Research, Berkshire, UK
    Appl Bioinformatics 2:63-6. 2003
    ..As a service to the immunobiology community, we have made a Perl implementation of the method available as a World Wide Web server...
  21. pmc Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
    Jesper Salomon
    The Jenner Institute, University of Oxford, Compton, Newbury, Berkshire, RG20 7NN, UK
    BMC Bioinformatics 7:501. 2006
    ..This paper introduces a kernel method that can handle variable length peptides effectively by quantifying similarities between peptide sequences and integrating these into the kernel...
  22. pmc Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102: a bioinformatic approach to the prediction of new epitopes
    Valerie A Walshe
    The Jenner Institute, University of Oxford, Compton, Berkshire, United Kingdom
    PLoS ONE 4:e8095. 2009
    ..Here, we describe the development and deployment of a reliable peptide-binding prediction method for a previously poorly-characterized human MHC class I allele, HLA-Cw*0102...
  23. ncbi request reprint Computational vaccinology: quantitative approaches
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG0 7NN, UK
    Novartis Found Symp 254:102-20; discussion 120-5, 216-22, 250-2. 2003
    ..Both methods are exemplified through their application to the well-studied problem of peptide binding to the human class I MHC molecule HLA-A*0201...
  24. ncbi request reprint JenPep: a novel computational information resource for immunobiology and vaccinology
    Helen McSparron
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, UK RG20 7NN
    J Chem Inf Comput Sci 43:1276-87. 2003
    ..Version 2.0 of the database is implemented in a bespoke postgreSQL database system and is fully searchable online via a perl/HTML interface (URL: http://www.jenner.ac.uk/JenPep)...
  25. ncbi request reprint Static energy analysis of MHC class I and class II peptide-binding affinity
    Matthew N Davies
    The Jenner Institute, University of Oxford, Berkshire, UK
    Methods Mol Biol 409:309-20. 2007
    ..The structures are remodeled, energy minimized, and annealed before the energetic interaction is calculated...
  26. ncbi request reprint Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation
    Irini Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, United Kingdom
    J Immunol 173:6813-9. 2004
    ..The reduction in the number of nonbinders varied from 10% (TAP-independent) to 33% (TAP-dependent), suggesting that TAP preselection is an important component in the successful in silico prediction of T cell epitopes...
  27. ncbi request reprint New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity
    Channa K Hattotuwagama
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    Org Biomol Chem 2:3274-83. 2004
    ..They can be used for the accurate prediction of T-cell epitopes and are freely available online ( http://www.jenner.ac.uk/MHCPred)...
  28. ncbi request reprint Coupling in silico and in vitro analysis of peptide-MHC binding: a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research Compton, High Street, Berkshire, Compton RG20 7NN, United Kingdom
    J Immunol 172:7495-502. 2004
    ....
  29. ncbi request reprint A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily
    Pingping Guan
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    Bioorg Med Chem 11:2307-11. 2003
    ..The present study demonstrated that CoMSIA is an effective tool for studying peptide-MHC interactions...
  30. pmc Toward the discovery of vaccine adjuvants: coupling in silico screening and in vitro analysis of antagonist binding to human and mouse CCR4 receptors
    Matthew N Davies
    The Jenner Institute, University of Oxford, Newbury, Berkshire, United Kingdom
    PLoS ONE 4:e8084. 2009
    ..An antagonist of the chemokine CCR4 receptor can display adjuvant-like properties by diminishing the ability of CD4+CD25+ regulatory T cells (Tregs) to down-regulate immune responses...
  31. pmc EpiJen: a server for multistep T cell epitope prediction
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, RG20 7NN, UK
    BMC Bioinformatics 7:131. 2006
    ..The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online...
  32. ncbi request reprint Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique
    Irini A Doytchinova
    The Jenner Institute, University of Oxford, Compton, Berkshire RG20 7NN, United Kingdom
    J Med Chem 49:2193-9. 2006
    ..Combinations of "aggressive" and "passive" amino acids in the middle part of epitopes constitute a putative TCR binding motif...
  33. doi request reprint Optimizing amino acid groupings for GPCR classification
    Matthew N Davies
    Edward Jenner Institute, Compton, Newbury, Berkshire, UK
    Bioinformatics 24:1980-6. 2008
    ..Local descriptors are a form of alignment-free analysis, the efficiency of which is dependent upon the correct selection of amino acid groupings...
  34. ncbi request reprint On the hierarchical classification of G protein-coupled receptors
    Matthew N Davies
    Edward Jenner Institute, Compton, Newbury, Berkshire, UK
    Bioinformatics 23:3113-8. 2007
    ..The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases...
  35. ncbi request reprint Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201
    Pingping Guan
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    J Med Chem 48:7418-25. 2005
    ..6 and 0.7 and r2 between 0.6 and 0.9). Further to the QSAR analysis, 15 peptides were synthesized and tested using a T2 stabilization assay. All peptides bound to HLA-A0201 well, and four peptides were identified as high-affinity binders...
  36. ncbi request reprint A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif
    Irini A Doytchinova
    Edward Jenner Istitute for Vaccine Research, Compton, Berkshire, RG20 7NN, UK
    J Comput Aided Mol Des 16:535-44. 2002
    ....
  37. pmc PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values
    Christopher P Toseland
    Edward Jenner Institute for Vaccine Research Compton, Berkshire, RG20 7NN, UK
    Nucleic Acids Res 34:D199-203. 2006
    ..The database can be found at the following URL: http://www.jenner.ac.uk/PPD...
  38. pmc Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity
    Matthew N Davies
    Edward Jenner Institute for Vaccine Research, Compton, Newbury, RG20 7NN, UK
    BMC Struct Biol 6:5. 2006
    ..Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions...
  39. pmc Benchmarking pK(a) prediction
    Matthew N Davies
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, RG20 7NN, UK
    BMC Biochem 7:18. 2006
    ..The pKa shift of a group from its intrinsic value is determined by the perturbation of the residue by the environment and can be calculated from three-dimensional structural data...
  40. pmc MHCPred: A server for quantitative prediction of peptide-MHC binding
    Pingping Guan
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire RG0 7NN, UK
    Nucleic Acids Res 31:3621-4. 2003
    ..MHCPred is available from the URL: http://www.jenner.ac.uk/MHCPred...
  41. ncbi request reprint Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding
    Irini A Doytchinova
    The Edward Jenner Institute for Vaccine Research, Compton RG20 7NN, UK
    Mol Immunol 43:2037-44. 2006
    ..The best model of proteasome cleavage was incorporated as the first step in a three-step algorithm for T-cell epitope prediction, where subsequent steps predicted TAP affinity and MHC binding using previously derived models...
  42. ncbi request reprint Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    J Proteome Res 1:263-72. 2002
    ..508 for this test set. The additive method was implemented in a program for rapid T-cell epitope search. It is universal and can be applied to any peptide-protein interaction where binding data is known...
  43. ncbi request reprint Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, RG20 7NN, Compton, Berkshire, UK
    J Comput Aided Mol Des 19:203-12. 2005
    ..The results suggest that, in their interactions with the MHC molecule, the peptide acts as a complicated ensemble of multiple amino acids mutually potentiating each other...
  44. ncbi request reprint Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique
    Channa K Hattotuwagama
    The Jenner Institute, University of Oxford, Compton, Berkshire, U K RG20 7NN
    J Chem Inf Model 46:1491-502. 2006
    ..The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred)...
  45. ncbi request reprint In silico prediction of peptide binding affinity to class I mouse major histocompatibility complexes: a comparative molecular similarity index analysis (CoMSIA) study
    Channa K Hattotuwagama
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, RG20 7NN, UK
    J Chem Inf Model 45:1415-23. 2005
    ..The peptides used in this study are available on the Internet (http://www.jenner.ac.uk/AntiJen). The partial least-squares method is available commercially in the SYBYL molecular modeling software package...
  46. ncbi request reprint HLA-A3 supermotif defined by quantitative structure-activity relationship analysis
    Pingping Guan
    Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire RG20 7NN, UK
    Protein Eng 16:11-8. 2003
    ..The influence of each of the 20 amino acids at each position of the peptide on binding was studied. A refined A3 supertype motif was defined in the study...
  47. ncbi request reprint Identifiying human MHC supertypes using bioinformatic methods
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, United Kingdom
    J Immunol 172:4314-23. 2004
    ....
  48. ncbi request reprint Quantitative structure-activity relationships and the prediction of MHC supermotifs
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire RG20 7NN, UK
    Methods 34:444-53. 2004
    ..For each superfamily, supermotifs defined by the two QSAR methods agree closely and are supported by many experimental data...
  49. ncbi request reprint Identification of the HLA-DM/HLA-DR interface
    Matthew N Davies
    Edward Jenner Institute, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford OX3 9DU, UK
    Mol Immunol 45:1063-70. 2008
    ..A possible dissociation mechanism is suggested by the presence of an acidic cluster near the N terminus of the bound peptide...
  50. pmc MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors
    Isabel K Macdonald
    The Jenner Institute, University of Oxford, Compton, Berkshire, United Kingdom
    PLoS Pathog 6:e1001149. 2010
    ....
  51. ncbi request reprint Immunoinformatics and the in silico prediction of immunogenicity. An introduction
    Darren R Flower
    The Jenner Institute, University of Oxford, Berkshire, UK
    Methods Mol Biol 409:1-15. 2007
    ..In thisbook, we introduce these subjects and explore the current state of play in immunoinformatics and the in silico prediction of immunogenicity...
  52. ncbi request reprint Receptor-ligand binding sites and virtual screening
    Channa K Hattotuwagama
    The Jenner Institute, University of Oxford, Compton, Berkshire RG20 7NN, UK
    Curr Med Chem 13:1283-304. 2006
    ....
  53. pmc In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination
    Jagadeesh Bayry
    The Edward Jenner Institute for Vaccine Research, University of Oxford, Compton, United Kingdom
    Proc Natl Acad Sci U S A 105:10221-6. 2008
    ..The significant adjuvant activity observed provides good evidence supporting our hypothesis that CCR4 is a viable target for rational adjuvant design...
  54. pmc DSD--an integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities
    Christopher P Toseland
    The Jenner Institute, University of Oxford, Compton, Berkshire, RG20 7NN, UK
    BMC Bioinformatics 6:283. 2005
    ..Stereo-selectivity is focused on the C4 hydrogen atoms of the nicotinamide ring of NAD(P). Depending upon which hydrogen is transferred at the C4 location, the enzyme is designated as A or B stereospecific...
  55. pmc GPCRTree: online hierarchical classification of GPCR function
    Matthew N Davies
    The Jenner Institute, University of Oxford, Compton, Newbury, Berkshire, RG20 7NN, UK
    BMC Res Notes 1:67. 2008
    ..Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence...
  56. ncbi request reprint Harnessing bioinformatics to discover new vaccines
    Matthew N Davies
    The Jenner Institute, University of Oxford, Compton, Berkshire, RG20 7NN, UK
    Drug Discov Today 12:389-95. 2007
    ..We also review current software developed to facilitate vaccine design...
  57. ncbi request reprint In silico identification of supertypes for class II MHCs
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, UK
    J Immunol 174:7085-95. 2005
    ..Apart from the good agreement between known binding motifs and our classification, several new supertypes, and corresponding thematic binding motifs, were also defined...
  58. pmc Benchmarking B cell epitope prediction: underperformance of existing methods
    Martin J Blythe
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
    Protein Sci 14:246-8. 2005
    ..Our results confirm the null hypothesis: Single-scale amino acid propensity profiles cannot be used to predict epitope location reliably. The implication for studies using such methods is obvious...
  59. ncbi request reprint Quantitative approaches to computational vaccinology
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, United Kingdom
    Immunol Cell Biol 80:270-9. 2002
    ..Both methods were exemplified through their application to the well-studied problem of peptides binding to the human class I MHC molecule HLA-A*0201...
  60. ncbi request reprint Receptor-binding sites: bioinformatic approaches
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, UK
    Methods Mol Biol 316:291-358. 2006
    ..Integration of both diverse experimental and diverse theoretical approaches is thus a mandatory requirement in the evaluation of binding sites and the binding events that occur within them...
  61. pmc Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response
    Nicola A Jones
    Viral Immunology Group, The Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire RG20 7NN, England, UK
    J Exp Med 200:1243-56. 2004
    ....
  62. pmc The lipocalin protein family: structure and function
    D R Flower
    Department of Physical Chemistry and BioAnalysis, Astra Charnwood, Loughborough, Leics, U K
    Biochem J 318:1-14. 1996
    ..The lipocalins have also been implicated in the regulation of cell homoeostasis and the modulation of the immune response, and, as carrier proteins, to act in the general clearance of endogenous and exogenous compounds...
  63. ncbi request reprint JenPep: a database of quantitative functional peptide data for immunology
    Martin J Blythe
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG0 7NN, UK
    Bioinformatics 18:434-9. 2002
    ..The compilation of quantitative binding data underlies attempts to derive tools for the accurate prediction of epitopes in cellular immunology and is part of our concerted goal to develop practical computational vaccinology...
  64. pmc BPROMPT: A consensus server for membrane protein prediction
    Paul D Taylor
    Edward Jenner Institute for Vaccine Research, Bioinformatics, Compton, Berkshire, UK
    Nucleic Acids Res 31:3698-700. 2003
    ..Topology predictions with accuracies of 70% for prokaryotes and 53% for eukaryotes were achieved. BPROMPT can be accessed at http://www.jenner.ac.uk/BPROMPT...
  65. ncbi request reprint Bacterial bioinformatics: pathogenesis and the genome
    Kelly Paine
    The Edward Jenner Institute for Vaccine Research, Newbury, Berkshire, United Kingdom
    J Mol Microbiol Biotechnol 4:357-65. 2002
    ..The combination of both fields should provide a rapid and efficient way of assisting in the future development of antimicrobial therapies...
  66. ncbi request reprint Modelling G-protein-coupled receptors for drug design
    D R Flower
    Department of Physical Sciences, Astra Charnwood, Bakewell Rd, Loughborough, Leicestershire, UK
    Biochim Biophys Acta 1422:207-34. 1999
    ..Aspects of this understanding, how these techniques can be used within a drug-design programme, and remaining challenges for the future are reviewed...
  67. ncbi request reprint Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction
    I A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK
    Bioinformatics 19:2263-70. 2003
    ..MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides...
  68. ncbi request reprint Toward the quantitative prediction of T-cell epitopes: coMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201
    I A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, RG20 7NN, UK
    J Med Chem 44:3572-81. 2001
    ....
  69. ncbi request reprint Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: a three-dimensional quantitative structure-activity relationship study
    Irini A Doytchinova
    Edward Jenner Institute for Vaccine Research, Compton, Berkshire, United Kingdom
    Proteins 48:505-18. 2002
    ..489. The coefficient contour maps identify the physicochemical property requirements at each position in the peptide molecule and suggest amino acid sequences for high-affinity binding to the HLA-A*0201 molecule...
  70. ncbi request reprint Proteomic applications of automated GPCR classification
    Matthew N Davies
    Edward Jenner Institute, Compton, Newbury, Berkshire, UK
    Proteomics 7:2800-14. 2007
    ..This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area...
  71. ncbi request reprint Novel perforin mutation in a patient with hemophagocytic lymphohistiocytosis and CD45 abnormal splicing
    James McCormick
    The Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, United Kingdom
    Am J Med Genet A 117:255-60. 2003
    ..Our findings suggest a combined role for perforin mutation and abnormal CD45 splicing as significant contributory factors in the pathogenesis of HLH...
  72. ncbi request reprint The lipocalin protein family: a role in cell regulation
    D R Flower
    Department of Physical Chemistry, Fisons plc, Pharmaceuticals Division, R and D Laboratories, Loughborough, Leicestershire, UK
    FEBS Lett 354:7-11. 1994
    ....
  73. ncbi request reprint The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods
    Pingping Guan
    Computational Biology Group, John Innes Centre, Norwich, UK
    Methods Mol Biol 409:143-54. 2007
    ..However, the reader should bear in mind that the methods have been incorporated into other software as well, such as SIMCA, statistiXL, and R...
  74. ncbi request reprint Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: can the alpha3 and beta2m domains be neglected?
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, UK
    J Comput Chem 25:1803-13. 2004
    ....
  75. ncbi request reprint Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, UK
    Philos Transact A Math Phys Eng Sci 363:2037-53. 2005
    ..The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines...
  76. ncbi request reprint Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, United Kingdom
    J Immunol 175:1715-23. 2005
    ..This enables us to simulate larger, more realistic biological systems for longer durations without the imposition of artificial constraints...
  77. ncbi request reprint Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics: comparison of discriminant analysis and multiple linear regression
    Irini A Doytchinova
    Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St, 1000 Sofia, Bulgaria
    J Chem Inf Model 47:234-8. 2007
    ..The new matrix was also tested on an external set of 160 binders to HLA-A*0201; it was able to recognize 135 (84%) of them...
  78. pmc FIMM, a database of functional molecular immunology: update 2002
    Christian Schonbach
    BIC KRDL, Kent Ridge Digital Labs, 21 Heng Mui Keng Terrace, 119613 Singapore
    Nucleic Acids Res 30:226-9. 2002
    ..FIMM has a set of search tools for extraction of information and results are presented as lists or as reports...
  79. ncbi request reprint Toward the atomistic simulation of T cell epitopes automated construction of MHC: peptide structures for free energy calculations
    Sarah J Todman
    Department of Crystallography, University of London, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
    J Mol Graph Model 26:957-61. 2008
    ..The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale...
  80. ncbi request reprint Toward an atomistic understanding of the immune synapse: large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Mol Immunol 45:1221-30. 2008
    ..Multi-scale molecular dynamics simulations may be the best opportunity we have to reach a full understanding of this remarkable supra-macromolecular event at a cell-cell junction...
  81. ncbi request reprint Molecular dynamics simulations: bring biomolecular structures alive on a computer
    Shunzhou Wan
    Centre for Computational Science, Chemistry Department, University College of London, UK
    Methods Mol Biol 409:321-39. 2007
    ..In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation...
  82. ncbi request reprint In silico prediction of peptide-MHC binding affinity using SVRMHC
    Wen Liu
    Department of Neuroscience, University of Minnesota, Minneapolis, USA
    Methods Mol Biol 409:283-91. 2007
    ..As a kernel-based learning method, SVRMHC has rendered models with demonstrated appealing performance in the practice of modeling peptide-MHC binding...
  83. doi request reprint Computer-aided biotechnology: from immuno-informatics to reverse vaccinology
    Sandro Vivona
    Molecular Biology and Bioinformatics Unit, Department of Biology, University of Padua, Padua, Italy
    Trends Biotechnol 26:190-200. 2008
    ..This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations...