Work
 Johnson & Johnson Pharmaceutical Research & Development
665 Stockton Drive
Exton, PA 19341
USA
Tel:  (610) 458-6045
Fax: (610) 458-8249
E-mail: dagrafio@prdus.jnj.com
URL: jnj.pharmarnd.com		 Home
 660 Perimeter Drive
Downingtown, PA 19335
USA
Tel: (610) 321-0106
E-mail: dimitris@dimitris-agrafiotis.com
URL: www.dimitris-agrafiotis.com

 

1990 - 1991 Harvard University
Postdoctoral Fellow
Research Advisor: Prof. Elias J. Corey (Nobel laureate in Chemistry, 1990)
 
1988 - 1990 University of California, Berkeley
Postdoctoral Fellow (Alexander Onassis Fellow)
Research Advisor: Prof. Andrew Streitwieser
 
1985 - 1988 Ph.D., Imperial College of Science & Technology, University of London
Theoretical Organic Chemistry (Alexander Onassis Fellow)
Research Advisor: Prof. Henry Rzepa
Thesis: “Molecular orbital studies of dihydrogen transfers and other reactions”
 
1981 - 1985 B.S., University of Patras, Greece
Chemistry
Research Advisor: Prof. Dionissios Papaioannou
Thesis: “Synthesis of methotrexate analogs”
 

 

2003 - Pres. Johnson & Johnson Pharmaceutical Research & Development, L.L.C.
Vice President, Informatics (2006 - )

Responsible for all information management systems for research & early development worldwide. Responsible for defining global information technology strategy and architecture for J&J pharmaceutical R&D. Management of a team of >70 employees and contractors. Methods and software development in the areas of computational drug design, chemoinformatics, data analysis, and visualization.

Johnson & Johnson Pharmaceutical Research & Development, L.L.C.
Senior Research Fellow & Team Leader, Molecular Design & Informatics (2003 - 2006)

Management of computer-assisted drug design and informatics groups (17 PhD, 3 MS) at the Exton, Cranbury and Spring House sites. Management of database and software systems supporting J&J's compound and screening logistics. Design and implementation of ABCD, a new global informatics framework for J&J PRD. Development of new algorithms for structure-based drug design, combinatorial chemistry, structure-activity correlation and virtual screening, and application of computational methods to J&J's internal discovery programs.

Indiana University School of Informatics, Bloomington
Adjunct Professor of Informatics
 
1994 - 2003. 3-Dimensional Pharmaceuticals, Inc.
Executive Director, Informatics

 Conception, design and implementation of DirectedDiversity®, an integrated, patented system for computer-assisted combinatorial drug design. Development of novel algorithms for the rapid enumeration and characterization of virtual libraries. Development of machine learning algorithms for structure-activity correlation and property prediction based on multivariate statistics, Bayesian methods, decision tress, case-based reasoning, neural networks, and fuzzy logic. Development of new algorithms for diversity assessment, compound selection, and multiobjective experiment planning based on simulated annealing, evolutionary programming and genetic algorithms. Application of novel optimization techniques based on artificial ant colony systems and particle swarms to structure-activity correlation, geometry optimization, and library design. Development of novel nonlinear mapping algorithms for massive data sets. Development of new methodologies for protein sequence analysis and classification. Development of new algorithms for encoding the human perception of molecular similarity. Development of new algorithms for conformational analysis, pharmacophore hypothesis generation, and biomolecular docking of large combinatorial libraries. Development of a comprehensive C++ foundation class library for molecular computation. Development of advanced graphical user interfaces for all the components of the DirectedDiversity® system. Development of integrated applications for high-throughput screening data reduction (Assay) and protein sequence analysis (Proteomica™). Homology modeling of G-protein coupled receptors. Design, implementation and management of 3DP's web-based DiscoverWorks informatics system. Application of DirectedDiversity® in 3DP’s internal and collaborative drug discovery efforts. Group (7 PhD, 3 MS) and project management.
 
1991 - 1994 Parke-Davis Pharmaceutical Research, Warner-Lambert Co. (now Pfizer Inc.)
Senior Scientist, Computer-Assisted Drug Design

Development of new parallel biomolecular docking algorithms based on simulated annealing and Darwinian evolution. Molecular modeling of growth factors. Pharmacophore modeling of selected antibacterial quinolones. Development of a large library of reusable software tools for molecular modeling applications.
 
1990 - 1991 Harvard University
Postdoctoral Fellow
Research Advisor: Prof. Elias J. Corey

Enhancements to the LHASA program for computer-assisted synthetic analysis. Development of a new suite of algorithms for the rapid three-dimensionalization of molecular structures, that allow LHASA to determine the stability of compounds generated in the course of a retrosynthetic analysis, to estimate equilibrium compositions and to determine the stereochemical outcome of reactions controlled by steric approach preferences .
 
1988 - 1990 University of California, Berkeley
Postdoctoral Fellow (Alexander Onassis Fellow)
Research Advisor: Prof. Andrew Streitwieser

Development of the electron density analysis program PRODEN. The program computes projected, planar and three-dimensional densities from ab initio wave-functions, and calculates atomic populations by demarkating and integrating the two-dimensional data. Development of graphics routines for rendering atomic virial surfaces and their PRODEN approximations, and integration into a portable general-use graphics package. Ab initio calculations on the solvation effects on the structure and electronic structure of lithium amide dimer, the pseudorotation mechanism of model phosphoranes, and the effects of adjacent heteroatoms in carbanion stability.
 
1985 - 1988 Imperial College of Science & Technology, University of London
Graduate Student (Alexander Onassis Fellow)
Research Advisor: Prof. Henry Rzepa

Theoretical SCF-MO investigation of the reaction mechanisms, substituent effects and kinetic isotope effects of dihydrogen transfers, dihydrogen eliminations, the Baeyer-Villiger and Stevens rearrangements and 2-azirine rearrangements, using semi-empirical and ab initio  theory. Implementation and evaluation of the Broyden-Fletcher-Goldfarb-Shanno variable metric minimization algorithm for geometry optimization, using the MNDO and AM1 procedures. Development of a portable computer graphics package for contouring, surface rendering and molecular plotting.

 

Computational chemistry and biology, computer-assisted drug design, combinatorial chemistry, molecular diversity, conformational analysis, protein docking, quantitative structure-activity relationships, artificial intelligence, computer-assisted organic synthesis, chemo- and bio-informatics, molecular orbital theory, algorithms, molecular graphics, software engineering.

 

1992 Residential School on Medicinal Chemistry
Drew University
 
2001 Bioinformatics: Principles, Methods and Applications
Massachusetts Institute of Technology
 

 

1986 - 1988 Imperial College of Science & Technology, University of London
Imperial College Computer Centre
Program Advisor, Teaching Assistant
 
1998 2-nd European Workshop in Drug Design
University of Siena, Italy
Faculty
 
2003 Innovative Combinatorial Approaches and Technologies
University of Florence, Italy
Faculty

 

2007 - pres Editorial Board, Journal of Chemical Information & Modeling
 
1999 - pres Editorial Board, Journal of Molecular Graphics & Modeling
 
2005 - pres

Editorial Board, Chemical Biology & Drug Design
 
2007 - pres Editorial Board, Molecular Diversity
 
2005 - pres

Board of Directors, International QSAR & Modeling Society (http://www.qsar.org/)
 
2007 - pres Board of Trustees, Chemical Structure Association Trust (http://www.csa-trust.org/)
 
2005 - pres Scientific Advisory Board, NIH Center for Chemoinformatics Research, Indiana University School of Informatics
 
2005 - pres Scientific Advisory Board, NIH Center for Chemoinformatics Research, University of North Carolina at Chapel Hill
 
2006 - pres Scientific Advisory Board, NIH Center for Chemoinformatics Research, Rensselaer Polytechnic Intitute
 
2005 - pres NIH Review Committee, NIH Roadmap, Computational Biophysics
 
2003 Scientific Advisory Board, IBC Conference on Design & Synthesis of Target Based Compound Libraries
 
2000 Guest Editor, Special Issue on Combinatorial Library Design, Journal of Molecular Graphics and Modelling
 
2004 Scientific Advisory Board, EuroQSAR 2004
 
2005 Scientific Advisory Board & Conference Organizer, Pacifichem 2005
 
2005-2011 Scientific Advisory Board, International Conference on Chemical Structures (ICCS)
 
1996 - pres Reviewer
Nature Rev., J. Med. Chem., J. Comput. Chem., J. Chem. Info. Comput. Sci., J. Mol. Graphics Modell., J. Comput. Aid. Mol. Des., Protein Eng., QSAR, SAR and QSAR Environ. Res.
 

 


 

1986 - 1988 Alexander Onassis Fellowship, Imperial College of Science & Technology
 
1988 - 1989 Alexander Onassis Fellowship, University of California, Berkeley
 
1999 Outstanding Achievement Award, 3-Dimensional Pharmaceuticals, Inc.
 
2005 J&J Image award (outstanding application of information technology)
 

 

American Chemical Society
American Association for the Advancement of Science
 Association of Greek Chemists
 


 

Date of Birth: May 30, 1964, in Athens, Greece
Citizenship: USA, Greece
Marital Status: Married to Konstadina Vlahogiani (Environmental Scientist), father of Iris (11) and Nephele (6).

 

Prof. Elias J. Corey
Department of Chemistry, Harvard University, Cambridge, MA 02138, USA
Tel: +1 (617) 495-4033
E-mail: corey@chemistry.harvard.edu

Prof. Michael Levitt
Chairman, Department of Structural and Cell Biology, Stanford University, Stanford, CA 94305, USA
Tel: +1 (415) 723-6800
E-mail: levitt@hyper.stanford.edu

Prof. Andrew Streitwieser
Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
Tel: +1 (415) 642-2204
E-mail: astreit@cmsa.berkeley.edu

Prof. Clarence Schutt
Department of Chemistry, Princeton University, Princeton, NJ 08544-1009, USA
Tel: +1 (609) 258-4435
E-mail: schutt@princeton.eduprinceton.edu

Dr. F. Raymond Salemme
Founder and former President and CEO of 3-Dimensional Pharmaceuticals, Inc.
1970 Timber Lake Drive
Yardley, PA 19067
Tel: +1 (215) 504-0836
E-mail: fsalemme1@comcast.net

Prof. Henry Rzepa
 Department of Chemistry, Imperial College of Science, Technology and Medicine, University of London, London, SW7 2AY, UK
Tel: +44 (171) 594-5774
E-mail: rzepa@ic.ac.uk

Dr. Alan Long
 Director, Department of Chemistry and Biochemistry, Harvard University, Cambridge, MA 02138, USA
Tel: +1 (617) 495-4283
E-mail: long@chemistry.harvard.edu

 

  1. D. K. Agrafiotis*, “Molecular orbital studies of dihydrogen transfers and other reactions”, Ph.D. Thesis, Department of Chemistry, Imperial College of Science & Technology, University of London, 1988.

  2. T. L. Graybill*, D. K. Agrafiotis, R. Bone, C. R. Illig, E. P. Jaeger, K. T. Locke, T. Lu, J. M. Salvino, R. M. Soll, J. C. Spurlino, N. Subasinghe, B. E. Tompczuk, and F. R. Salemme, “Enhancing the drug discovery process by integration of high-throughput chemistry and structure-based drug design”, in Molecular Diversity and Combinatorial Chemistry, Chaiken, I. M, and Janda, K. D., Eds., ACS, Washington D. C., 1996, 16-26.

  3. D. K. Agrafiotis*, “Diversity of chemical libraries”, in The Encyclopedia of Computational Chemistry; Schleyer, P.v.R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R., Eds., John Wiley and Sons, Chichester, 1998, Vol. 1, 742-761. [PDF]

  4. D. K. Agrafiotis*, J. P. Myslik, and F. R. Salemme, “Advances in diversity profiling and combinatorial series design”, in Annual Reports in Combinatorial Chemistry and Molecular Diversity, Pavia, M., and Moos, W., Eds., Kluwer, 1999, 2, 71-92.

  5. D. K. Agrafiotis*, V. S. Lobanov, D. N. Rassokhin, and S. Izrailev, “The measurement of molecular diversity”, in Virtual Screening of Bioactive Molecules, Böhm, H.-J., and Schneider, G., Eds., Wiley-VCH, Weinheim, 2000, 265-300.

  6. M. Farnum, R. DesJarlais, and D. K. Agrafiotis*, "Molecular diversity", in Chemoinformatics - From Data to Knowledge, Gasteiger, J., Ed., John Wiley and Sons, Chichester, 2003 (in press).

  7. A. C. Gibbs, and D. K. Agrafiotis*, "Chemical diversity: definition and quantification", in Exploiting Chemical Diversity for Drug Discovery, Bartlett, P., Entzeroth, M., Eds., The Royal Society of Chemistry, 2006, 139-160.
     

  1. D. K. Agrafiotis, and H. S. Rzepa*, "Dihydrogen transfer reactions. An SCF-MO study of the relative energies of the concerted and stepwise pathways.", J. Chem. Soc., Chem. Commun., 1987, 902

  2. D. K. Agrafiotis, and H. S. Rzepa*, "Evaluation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) variable metric method in geometry optimisation using semi-empirical SCF-MO procedures.", J. Chem. Research (S), 1988, 101.

  3. D. K. Agrafiotis, and H. S. Rzepa*, "A theoretical MNDO and AM1 SCF-MO study of dihydrogen elimination reactions.", J. Chem. Soc., Perkin Trans. II, 1989, 367.

  4. D. K. Agrafiotis, and H. S. Rzepa*, "A theoretical MNDO and AM1 SCF-MO study of dihydrogen transfer reactions", J. Chem. Soc., Perkin Trans. II, 1989, 475.

  5. D. K. Agrafiotis*, A. Streitwieser, and H. S. Rzepa, “MOECULE: GKS graphical display package”, QCPE Bull., 1989, 9, 127, Program 583.

  6. P. Wang, D. K. Agrafiotis, A. Streitwieser*, and P. v. R. Schleyer*, "Berry and turnstyle processes in the preudorotation of three phosphoranes."J. Chem. Soc., Chem. Commun., 1990, 201.

  7. D. K. Agrafiotis, B. L. Tansy and A. Streitwieser*, "PRODEN, a new electron density analysis program.", J. Comp. Chem., 1990, 11(9), 1101.

  8. D. K. Agrafiotis*, B. Tansy, and A. Streitwieser, “PRODEN: A new electron density analysis program”, QCPE Bull., 1991, 11, 13, Program 600.

  9. K. Spiegel, D. K. Agrafiotis, B. Carpathe, R. E. Davis, M. R. Dickerson, J. H. Fergus, T. W. Hepburn, J. S. Marks, M. van Dorf, D. M. Wieland, and J. C. Jaen*, “PD 90780, a non-peptide inhibitor of nerve growth factor’s binding to the P75 NGF receptor”, Biochem. Biophys. Res. Comm., 1995, 217(2), 488.

  10. D. K. Agrafiotis*, “Stochastic algorithms for maximizing molecular diversity”, 3-rd Electronic Computational Chemistry Conference, 1996.

  11. D. K. Agrafiotis*, “A new method for analyzing protein sequence relationships based on Sammon maps”, Protein Sci., 1997, 6(2), 287. [PDF]

  12. D. K. Agrafiotis*, “On the use of information theory for assessing molecular diversity”, J. Chem. Info. Comp. Sci., 1997, 37(3), 576. [PDF]

  13. D. K. Agrafiotis*, “Stochastic algorithms for maximizing molecular diversity”, J. Chem. Info. Comp. Sci., 1997, 37(5), 841. [PDF]

  14. D. K. Agrafiotis*, J. P. Myslik, and F. R. Salemme, “Advances in diversity profiling and combinatorial series design”, Mol. Diversity, 1999, 4, 1-22. [PDF]

  15. D. K. Agrafiotis*, and V. S. Lobanov, “An efficient implementation of distance-based diversity metrics based on k-d trees”, J. Chem. Info. Comp. Sci., 1999, 39(1), 51-58. [PDF]

  16. V. S. Lobanov*, and D. K. Agrafiotis, “Stochastic similarity selections from large combinatorial libraries”, J. Chem. Info. Comput. Sci., 2000, 40, 460-470. [PDF]

  17. D. K. Agrafiotis*, and V. S. Lobanov, “Ultrafast algorithm for designing focused combinatorial arrays”, J. Chem. Info. Comput. Sci., 2000, 40, 1030-1038. [PDF]

  18. D. B. Boyd, D. K. Agrafiotis, and E. J. Martin, "Introduction and forward to the special issue on combinatorial library design", J. Mol. Graphics Modell., 2000, 18, 317-319.

  19. D. N. Rassokhin, and D. K. Agrafiotis*, “Kolmogorov-Smirnov statistic and its applications in library design”, J. Mol. Graphics Modell., 2000, 18(4-5), 370-384. [PDF]

  20. D. K. Agrafiotis*, and V. S. Lobanov, “Nonlinear mapping networks”, J. Chem. Info. Comput. Sci., 2000, 40, 1356-1362. [PDF]

  21. D. K. Agrafiotis*, “A constant time algorithm for estimating the diversity of large chemical libraries”, J. Chem. Info. Comput. Sci., 2001, 41(1), 159-167 [PDF].

  22. S. Izrailev*, and D. K. Agrafiotis, “A new method for building regression tree models for QSAR based on artificial ant colony systems”, J. Chem. Info. Comput. Sci., 2001, 41(1), 176-180. [PDF]

  23. D. N. Rassokhin, V. S. Lobanov, and D. K. Agrafiotis*, “Nonlinear mapping of massive data sets by fuzzy clustering and neural networks”, J. Comput. Chem., 2001, 22(4), 373-386. [PDF]

  24. D. K. Agrafiotis*, D. N. Rassokhin, V. S. Lobanov, “Multidimensional scaling and visualization of large molecular similarity tables”, J. Comput. Chem., 2001, 22(5), 488-500. [PDF]

  25. D. K. Agrafiotis* and D. N. Rassokhin, "Design and prioritization of plates for high-throughput screening", J. Chem. Info. Comput. Sci., 2001, 41(3), 798-805. [PDF]

  26. D. K. Agrafiotis*, “Multiobjective optimization of combinatorial libraries”, IBM J. Res. Develop., 2001, 45(3/4), 545-566. ( Special Issue on Deep Computing in the Life Sciences). [PDF]

  27. V. S. Lobanov* and D. K. Agrafiotis, “Combinatorial networks”, J. Mol. Graphics Modell., 2001, 19(6), 571-578. [PDF]

  28. D. K. Agrafiotis and V. S. Lobanov*, "Multidimensional scaling of combinatorial libraries without explicit enumeration", J. Comput. Chem., 2001, 22(14), 1712-1722. [PDF]

  29. S. Izrailev*, and D. K. Agrafiotis, "Variable selection for QSAR by artificial ant colony systems", SAR and QSAR in Environ. Res., 2002, 13, 417-423. [PDF]

  30. D. K. Agrafiotis*, and D. N. Rassokhin, "A fractal approach for selecting an appropriate bin size for cell-based diversity estimation", J. Chem. Info. Comput. Sci., 2002, 42, 117-122. [PDF]

  31. V. S. Lobanov* and D. K. Agrafiotis, “Scalable methods for the construction and analysis of virtual combinatorial libraries”, Combin. Chem. High-Throughput Screen., 2002, 5, 167-178. [PDF]

  32. D. K. Agrafiotis*, and W. Cedeño, "Feature selection for structure-activity correlation using binary particle swarms", J. Med. Chem., 2002, 45, 1098-1107. [PDF]

  33. D. K. Agrafiotis*, V. S. Lobanov, and F. R. Salemme, "Combinatorial informatics in the post-genomics era, Nature Rev. Drug Discov., 2002, 1, 337-346. [PDF]

  34. D. K. Agrafiotis*, W. Cedeño, and V. S. Lobanov, "On the use of neural network ensembles in QSAR and QSPR", J. Chem. Info. Comput. Sci., 2002, 42, 903-911. [PDF]

  35. H. Xu*, and D. K. Agrafiotis, "Retrospect and prospect of virtual screening in drug lead discovery", Curr. Topics Med. Chem., 2002, 2, 1305-1320. [PDF]

  36. D. K. Agrafiotis*, “Multiobjective optimization of combinatorial libraries”, J. Comput. Aid. Mol. Des., 2002, 16, 335-356. [PDF]

  37. W. Cedeño, and D. K. Agrafiotis, "Combining particle swarms and k-nearest neighbors for the development of quantitative structure-activity relationships", Int. J. Comput. Res., 2002, 11, 443-452. [PDF]

  38. W. Cedeño* and D. K. Agrafiotis, "Application of niching particle swarms to QSAR and QSPR", Proceedings of the 14-th European Symposium on QSAR, Bournemouth, UK, September 8-13, 2002. [PDF]

  39. D. K. Agrafiotis,* and H. Xu, "A self-organizing principle for learning nonlinear manifolds", Proc. Natl. Acad. Sci. USA, 2002, 99, 15869-15872. [PDF]

  40. D. K. Agrafiotis*, "Stochastic proximity embedding", J. Comput. Chem., 2003, 24, 1215-1221. [PDF]

  41. D. K. Agrafiotis*, and H. Xu, "A geodesic framework for analyzing molecular similarities", J. Chem. Info. Comput. Sci., 2003, 43, 475-484. [PDF]

  42. W. Cedeño*, and D. K. Agrafiotis, "Using particle swarms for the development of QSAR models based on k-nearest neighbor and kernel regression", J. Comput. Aid. Mol. Des., 2003, 17, 255-263. [PDF]

  43. D. N. Rassokhin* and D. K. Agrafiotis, "A modified update rule for stochastic proximity embedding", J. Mol. Graphics Modell., 2003, 22, 133-140. [PDF]

  44. M. Farnum, H. Xu and D. K. Agrafiotis*, "Exploring the nonlinear geometry of sequence homology", Protein Sci., 2003, 12, 1604-1612. [PDF]

  45. H. Xu, S. Izrailev, and D. K. Agrafiotis*, "Conformational sampling by self-organization", J. Chem. Info. Comput. Sci., 2003, 43, 1186-1191. [PDF]

  46. H. Xu*, and D. K. Agrafiotis, "Nearest neighbor search in general metric spaces using a tree data structure with a simple heuristic", J. Chem. Info. Comput. Sci., 2003, 43, 1933-1941. [PDF]

  47. S. Izrailev*, and D. K. Agrafiotis, "A method for quantifying and visualizing the diversity of QSAR models", J. Mol. Grphics Modell., 2004, 22, 275-284. [PDF]

  48. M. Seierstad*, and D. K. Agrafiotis, "A QSAR model of hERG binding using a large, diverse and internally consistent training set", Chem. Biol. Drug Des., 2006, 67(4), 284-296. [PDF]

  49. S. Izrailev, F. Zhu, and D. K. Agrafiotis*, "A distance geometry heuristic for expanding the range of geometries sampled during conformational search", J. Comput. Chem., 2006, 27(16), 1962-1969. [PDF]

  50. M. F. M. Engels*, A. Gibbs, E. P. Jaeger, D. Verbinnen, V. S. Lobanov, and D. K. Agrafiotis, "A clustering method for assessing the overlap between large chemical libraries and its application to a recent acquisition", J. Chem. Info. Model., 2006, 46, 2651-2660. [PDF]

  51. D. K. Agrafiotis*, A. Gibbs, F. Zhu, S. Izrailev, and E. Martin, "Conformational boosting", Aust. J. Chem. (special issue on Pacifichem 2005), 2006, 59, 874-878. [PDF]

  52. D. K. Agrafiotis*, D. Bandyopadhyay, and M. Farnum, "Radial clustergrams: visualizing the aggregate properties of hierarchical clusters", J. Chem. Info. Model., 2007, 47, 69-75. [PDF]

  53. F. Zhu*, and D. K. Agrafiotis, "A self-organizing superposition (SOS) algorithm for conformational sampling", J. Comput. Chem., 2007, 28, 1234-1239. [PDF]

  54. D. K. Agrafiotis*, A. Gibbs, F. Zhu, S. Izrailev, and E. Martin, "Conformational sampling of bioactive molecules: a comparative study", J. Chem. Info. Model., 2007, 47, 1067-1086. [PDF]

  55. D. K. Agrafiotis*, D. Bandyopadhyay, J. Wegner, and H. Van Vlijmen, "Recent advances in chemoinformatics", J. Chem. Info. Model., 2007, 47, 1279-1293. [PDF]

  56. F. Zhu*, and D. K. Agrafiotis, "Recursive distance partitioning algorithm for common pharmacophore identification", J. Chem. Info. Model., 2007, 47, 1619-1625. [PDF]

  57. D. K. Agrafiotis*, D. Bandyopadhyay, G. Carta, A. J. S. Knox, and D. G. Lloyd, "On the effects of permuted input on conformational sampling of druglike molecules: an evaluation of stochastic proximity embedding (SPE)", Chem. Biol. Drug Des., 2007, 70(2), 123-133. [PDF]

  58. D. Bandyopadhyay, and D. K. Agrafiotis*, "A self-organizing algorithm for molecular alignment and pharmacophore development", J. Comput. Chem., 2007, in press.

  59. D. K. Agrafiotis*, M. Shemanarev, P. J. Connolly, M. Farnum, and V. S. Lobanov, "SAR maps: a new SAR visualization technique for medicinal chemists", J. Med. Chem., 2007, 50(24), 5926-5937.

  60. D. K. Agrafiotis*, et al., "Advanced Biological and Chemical Discovery (ABCD): centralizing discovery knowledge in an inherently decentralized world", J. Chem. Info. Model., 2007, 47, 1999-2014.


    UNDER REVIEW
     


  61.  

  1. D. K. Agrafiotis, R. Bone, F. R. Salemme and R. Soll. “System and method for automatically generating chemical compounds with desired properties”. US Patent 5,463,564, October 31, 1995. [USPTO]

  2. D. K. Agrafiotis, R. Bone, F. R. Salemme and R. Soll. “System and method for automatically generating chemical compounds with desired properties”. US Patent 5,574,656, November 12, 1996. [USPTO]

  3. D. K. Agrafiotis, R. Bone, F. R. Salemme and R. Soll. “System, method and computer program for at least partially automatically generating chemical compounds having desired properties”. US Patent 5,684,711, November 4, 1997. [USPTO]

  4. D. K. Agrafiotis, R. Bone, F. R. Salemme and R. Soll. “System, method and computer program for at least partially automatically generating chemical compounds with desired properties from a list of potential chemical compounds to synthesize”. US Patent 5,901,069, May 4, 1999. [USPTO]

  5. D. K. Agrafiotis, and F. R. Salemme. “Method, system, and computer program product for representing similarity/dissimilarity between chemical compounds”. US Patent 6,295,514, September 25,2001. [USPTO]

  6. D. K. Agrafiotis, R. Bone, F. R. Salemme and R. Soll. “System, method and computer program product for identifying chemical compounds with desired properties”. US Patent 6,421,612, July 16,2002. [USPTO]

  7. D. K. Agrafiotis, R. Bone, F. R. Salemme and R. Soll. “Methodof generating chemical compounds having desired properties”. US Patent 6,434,490, August 13,2002. [USPTO]

  8. D. K. Agrafiotis, V. S. Lobanov, and F. R. Salemme. "System, method, and computer program product for representing proximity data in a multidimensional space". US Patent 6,453,246, September 17, 2002. [USPTO]

  9. D. S. Dhanoa, D. Doller, S. Meegalla, R. M. Soll, D. K. Agrafiotis, N. Wisnewski, G. M. Silver, D. T. Stinchcomb, and R. L. Seward. "Use of 1,3-substituted pyrazol-5-yl sulfonates as pesticides". US Patent 6,506,784, January 14, 2003. [USPTO]

  10. S. Meegalla, D. K. Agrafiotis, D. Dhanoa, D. Doller, R. Soll, N. Wisnewski, G. Silver, D. Stinchcomb, R. L. Seward, and D. Sha. "1-aryl-3-thioalkyl pyrazoles, and the synthesis thereof and use thereof as insecticides". US Patent 6,518,266, February 11, 2003. [USPTO]

  11. D. K. Agrafiotis, V. S. Lobanov, and F. R. Salemme. "Method, system and computer program product for nonlinear mapping of multidimensional data". US Patent 6,571,227, May 27, 2003. [USPTO]

  12. D. K. Agrafiotis, V. S. Lobanov, and F. R. Salemme. "Method and computer program product for designing combinatorial arrays". US Patent 6,671,627, December 30, 2003. [USPTO]

  13. D. K. Agrafiotis, V. S. Lobanov, and F. R. Salemme. "Method, system, and computer program product for encoding and building products of a virtual combinatorial library". US Patent 6,678,619, January 13, 2004. [USPTO]

  14. V. S. Lobanov, D. K. Agrafiotis, and F. R. Salemme. "Method, system, and computer program product for determining properties of combinatorial library products from features of library building blocks". US Patent 6,834,239, December 21, 2004. [USPTO]

  15. D. K. Agrafiotis, D. N. Rassokhin, V. S. Lobanov, and F. R. Salemme. "System, method, and computer program product for representing object relationships in a multidimensional space". US Patent 7,039,621, May 2, 2006. [USPTO]

  16. D. K. Agrafiotis, V. S. Lobanov, and F. R. Salemme. "Method, system, and computer program product for analyzing combinatorial libraries". US Patent 7,054,757, June 13, 2006. [USPTO]

  17. D. K. Agrafiotis, V. S. Lobanov, and F. R. Salemme. "Method, system and computer program product for non-linear mapping of multi-dimensional data". US Patent 7,117,187, October 3, 2006. [USPTO]

  18. D. K. Agrafiotis, D. N. Rassokhin, V. S. Lobanov, and F. R. Salemme. "System, method, and computer program product for representing object relationships in a multidimensional space". US Patent 7,139,739, November 21, 2006. [USPTO]

    UNDER REVIEW
     
    Several patent applications are currently under review.
       


SELECTED
 

  1. D. K. Agrafiotis and E. P. Jaeger, 212-th ACS National Meeting, March 24-28, 1996, New Orleans, LA. “DirectedDiversity: an operating system for combinatorial chemistry”.

  2. D. K. Agrafiotis, 213-th ACS National Meeting, April 13-17, 1997, San Francisco, CA. “Stochastic algorithms for assessing molecular diversity”.

  3. D. K. Agrafiotis, 9-th International Congress of Quantum Chemistry, June 3-7, 1997, Savannah, GA. “Computer-aided combinatorial drug design”.

  4. D. K. Agrafiotis, 1997 Gordon Conference on QSAR, August 3-8, 1997, Tilton, NH. “Systems and methods for designing combinatorial chemistry experiments”.

  5. D. K. Agrafiotis, DuPont Central Research & Development, Wilmington, DE, December 17, 1997. “Thinking machines in drug design: the challenge of combinatorial chemistry”.

  6. D. K. Agrafiotis, and V. S. Lobanov, 215-th ACS National Meeting, March 29 - April 2, 1998, Dallas, TX. “Bridging the gap between diversity and QSAR”.

  7. D. K. Agrafiotis, and V. S. Lobanov, Computational Approaches to the Design and Analysis of Combinatorial Libraries, MGMS/CSA Meeting, April 14-16, 1998, Sheffield, England. “A rational approach for combinatorial drug design”.

  8. D. K. Agrafiotis, and V. S. Lobanov, 217-th ACS National Meeting, March 21-25, 1999, Anaheim, CA. “Meta-QSAR”.

  9. D. K. Agrafiotis, PacifiChem 2000, Symposium on Mathematical Aspects of Drug Design, Honolulu, Hawaii, December 14-18, 2000.

  10. D. K. Agrafiotis, DIMACS Series on Computational Molecular Biology, Rutgers University, June 21-22, 2001. "Multidimensional scaling of massive data sets".

  11. D. K. Agrafiotis, 2002 Gordon Conference on Computational Chemistry, June 30-July 5, 2002, Colby-Sawyer College, NH. "Stochastic proximity embedding".

  12. D. K. Agrafiotis, Princeton University, February 21, 2003, Princeton, NJ. "Molecular informatics in the new millennium".

  13. D. K. Agrafiotis, and H. Xu,225-th ACS National Meeting, March 23-27, 2003, New Orleans, LA. “A self-organizing algorithm for extracting the intrinsic dimensionality of large high-dimensional data”.

  14. D. K. Agrafiotis, Cornell University, April 25, 2003, Ithaca, NY. "New algorithms for the analysis of large data sets and their application in molecular design".

  15. D. K. Agrafiotis, Accelrys World, March 8-10, 2004, San Diego, CA. "A self-organizing alternative to distance geometry".

  16. D. K. Agrafiotis, NIH - Chemistry & Biology: Partners in Decoding the Genome, March 15-16, 2004, Bethesda, MD. "Molecular informatics for the new drug discovery enterprise". 

  17. D. K. Agrafiotis, Indiana University, March 24, 2004, Bloomington, IN. "Molecular informatics for the new drug discovery enterprise".

  18. D. K. Agrafiotis, 230-th ACS National Meeting, August 28-September 1, 2005, Washngton, DC. “Visualizing structure-activity relationships in ABCD”.

  19. D. K. Agrafiotis, 2005 Gordon Conference on Combinatorial and High Throughput Materials Development, August 14-19, 2005, Oxford, UK. “Computational tools for the design and analysis of massive combinatorial libraries”.

  20. D. K. Agrafiotis, EMBL/EBI Conference on Therapeutic Applications of Computational Biology, September 4-6, 2005, Hinxton, UK. "Design and analysis of large chemical libraries for lead discovery & optimization".

  21. D. K. Agrafiotis, University of Toronto, September 22, 2005, Toronto, Canada. "New algorithms for the analysis of large data sets and their application in molecular design".

  22. D. K. Agrafiotis, 1-st German Conference on Chemoinformatics, November 13-15, 2005, Goslar, Germany. "A new clustering algorithm for general metric spaces".

  23. D. K. Agrafiotis, University of Erlangen, November 16, 2005, Erlangen, Germany. "Modeling complexity: from stochastic proximity embedding to ABCD".

  24. D. K. Agrafiotis, Pacifichem 2005, December 15-20, 2005, Honolulu, HI. "A self-organizing principle for modeling proximity data".

  25. D. K. Agrafiotis, Plenary Talk, Smart Lab 2007, February 27-28, 2007, London, UK. "ABCD: centralizing .data in an inherently decentralized world".

  26. D. K. Agrafiotis, Plenary Talk, Discovery Knowledge & Informatics, April 24-25, 2007, Amsterdam, The Netherlands. TBD.

  27. D. K. Agrafiotis, A. Gibbs, F. Zhu, and E. Martin, 233-rd ACS National Meeting, March 25-29, 2007, Chicago, IL. "Advances in conformational sampling".

  28. D. K. Agrafiotis, MBI Chemogenomics Workshop, Mathematical Biosciences Institute, Ohio State University, May 8-9, 2007, Columbus, OH. "New algorithms for mining large data sets".

  29. D. K. Agrafiotis, Plenary Talk, SIAM Conference on Mathematics for Industry: Challenges & Frontiers, October 9-11, 2007, Philadelphia, PA. TBD.