1. Agrafiotis DK*. 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. Graybill TL*, Agrafiotis DK,
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3. Agrafiotis DK*. Diversity of
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5. Agrafiotis DK*, Lobanov VS, Rassokhin DN, Izrailev S. The measurement of molecular diversity. In Virtual
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8. Krein M, Huang T-W,
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9. Agrafiotis DK, Rzepa HS*. Evaluation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) variable metric method in geometry
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10. Agrafiotis DK, Rzepa HS*. A theoretical MNDO and AM1 SCF-MO study of dihydrogen
elimination reactions. J. Chem. Soc., Perkin Trans. II 1989, 367.
11. Agrafiotis DK, Rzepa HS*. A theoretical MNDO and AM1 SCF-MO study of dihydrogen
transfer reactions. J. Chem. Soc.,
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12. Agrafiotis DK*, Streitwieser
A, Rzepa HS, MOLECULE: A GKS graphical display package. QCPE Bull. 1989, 9, 127, Program 583.
13. Wang P, Agrafiotis DK,
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Berry and turnstyle processes in the preudorotation of three phosphoranes.
J. Chem. Soc., Chem. Commun. 1990, 201.
14. Agrafiotis DK, Tansy BL, Streitwieser A*. PRODEN, a new electron density analysis
program. J. Comp. Chem. 1990, 11(9), 1101.
15. Agrafiotis DK*, Tansy B, Streitwieser A. PRODEN: A new electron density analysis program. QCPE Bull. 1991, 11, 13, Program 600.
16. Spiegel K, Agrafiotis DK,
Carpathe B, Davis RE, Dickerson MR, Fergus JH,
Hepburn TW, Marks JS, Van Dorf M, Wieland DM, Jaen
JC*. 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.
17. Agrafiotis DK*. Stochastic
algorithms for maximizing molecular diversity. 3-rd Elec. Comput. Chem. Conf. 1996.
18. Agrafiotis DK*. A new method
for analyzing protein sequence relationships based on Sammon
maps. Protein Sci. 1997, 6(2), 287. [PDF]
19. Agrafiotis DK*. On the use of
information theory for assessing molecular diversity. J. Chem. Info. Comp.
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20. Agrafiotis DK*. Stochastic
algorithms for maximizing molecular diversity. J. Chem. Info. Comp. Sci. 1997,
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21. Agrafiotis DK*, Myslik JP, Salemme FR. Advances in diversity profiling and
combinatorial series design. Mol. Diversity 1999, 4, 1-22.
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22. Agrafiotis DK*, Lobanov VS. An
efficient implementation of distance-based diversity metrics based on k-d
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23. Lobanov VS*, Agrafiotis DK.
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24. Agrafiotis DK*, Lobanov VS.
Ultrafast algorithm for designing focused combinatorial arrays. J. Chem.
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25. Boyd DB, Agrafiotis DK, Martin EJ.
Introduction and forward to the special issue on combinatorial library design. J.
Mol. Graphics Modell. 2000, 18,
317-319.
26. Rassokhin DN, Agrafiotis DK*. Kolmogorov-Smirnov
statistic and its applications in library design. J. Mol. Graphics Modell. 2000, 18(4-5), 370-384. [PDF]
27. Agrafiotis DK*, Lobanov VS.
Nonlinear mapping networks. J. Chem. Info. Comput.
Sci. 2000, 40, 1356-1362. [PDF]
28. Agrafiotis DK*. A constant
time algorithm for estimating the diversity of large chemical libraries. J.
Chem. Info. Comput. Sci. 2001, 41(1),
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29. Izrailev S*, Agrafiotis DK.
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]
30. Rassokhin DN, Lobanov VS, Agrafiotis DK*. Nonlinear mapping of massive data
sets by fuzzy clustering and neural networks. J. Comput.
Chem. 2001, 22(4), 373-386. [PDF]
31. Agrafiotis DK*, Rassokhin DN, Lobanov VS. Multidimensional scaling and visualization of large molecular
similarity tables. J. Comput. Chem. 2001,
22(5), 488-500. [PDF]
32. Agrafiotis DK*, Rassokhin DN. Design and prioritization of plates for high-throughput screening. J.
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33. Agrafiotis DK*. Multiobjective optimization of
combinatorial libraries. IBM J. Res. Develop. 2001, 45(3/4),
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34. Lobanov VS*, Agrafiotis
DK. Combinatorial networks. J. Mol. Graphics Modell.
2001, 19(6), 571-578. [PDF]
35. Agrafiotis DK, Lobanov VS*.
Multidimensional scaling of combinatorial libraries without explicit
enumeration. J. Comput. Chem. 2001, 22(14),
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36. Izrailev S*, Agrafiotis DK.
Variable selection for QSAR by artificial ant colony systems. SAR and QSAR
in Environ. Res. 2002, 13, 417-423. [PDF]
37. Agrafiotis DK*, Rassokhin DN. A fractal approach for selecting an appropriate bin size for
cell-based diversity estimation. J. Chem. Info. Comput.
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38. Lobanov VS*, Agrafiotis DK.
Scalable methods for the construction and analysis of virtual combinatorial
libraries. Combin. Chem. High-Throughput
Screen. 2002, 5, 167-178. [PDF]
39. Agrafiotis DK*, Cedeño W. Feature selection
for structure-activity correlation using binary particle swarms. J. Med.
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40. Agrafiotis DK*, Lobanov VS, Salemme FR. Combinatorial informatics in the
post-genomics era. Nature Rev. Drug Discov. 2002,
1, 337-346. [PDF]
41. Agrafiotis DK*, Cedeño W, and Lobanov VS. On
the use of neural network ensembles in QSAR and QSPR. J. Chem. Info. Comput. Sci. 2002, 42, 903-911. [PDF]
42. Xu H*, and Agrafiotis DK. Retrospect and
prospect of virtual screening in drug lead discovery. Curr.
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43. Agrafiotis DK*. Multiobjective optimization of
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44. Cedeño W, Agrafiotis DK. Combining particle
swarms and k-nearest neighbors for the development of quantitative
structure-activity relationships. Int. J. Comput.
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45. Cedeño W*, Agrafiotis DK. 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]
46. Agrafiotis DK*,
Xu H. A self-organizing principle for learning nonlinear manifolds. Proc.
Natl. Acad. Sci. USA, 2002, 99, 15869-15872. [PDF]
47. Agrafiotis DK*. Stochastic proximity embedding. J. Comput. Chem. 2003, 24, 1215-1221. [PDF]
48. Agrafiotis DK*, Xu H. A geodesic framework for analyzing molecular
similarities. J. Chem. Info. Comput. Sci. 2003,
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49. Cedeño W*, Agrafiotis DK. Using particle
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kernel regression. J. Comput. Aid. Mol. Des. 2003,
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50. Rassokhin DN*, Agrafiotis DK. A modified update
rule for stochastic proximity embedding. J. Mol. Graphics Modell. 2003, 22, 133-140. [PDF]
51. M. Farnum, Xu H, Agrafiotis DK*. Exploring the nonlinear geometry of
sequence homology. Protein Sci. 2003, 12, 1604-1612. [PDF]
52. Xu H, Izrailev S, Agrafiotis DK*. Conformational sampling by
self-organization. J. Chem. Info. Comput. Sci. 2003,
43, 1186-1191. [PDF]
53. Xu H*, Agrafiotis DK. 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]
54. Izrailev S*, Agrafiotis DK. A method for
quantifying and visualizing the diversity of QSAR models. J. Mol. Grphics Modell. 2004, 22,
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55. Seierstad M*, Agrafiotis DK. 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]
56. Izrailev S, Zhu F, Agrafiotis DK*. A distance geometry heuristic for
expanding the range of geometries sampled during conformational search. J. Comput. Chem. 2006, 27(16), 1962-1969. [PDF]
57. Engels MFM*, Gibbs A,
Jaeger EP, Verbinnen D, Lobanov VS, Agrafiotis
DK. 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]
58. Agrafiotis DK*, A. Gibbs, Zhu F, Izrailev S, Martin E. Conformational
boosting. Aust. J. Chem. 2006, 59, 874-878. [PDF]
59. Agrafiotis DK*, Bandyopadhyay D, Farnum M. Radial clustergrams:
visualizing the aggregate properties of hierarchical clusters. J. Chem.
Info. Model. 2007, 47, 69-75. [PDF]
60. Zhu F*, Agrafiotis DK. A self-organizing
superposition (SOS) algorithm for conformational sampling. J. Comput. Chem. 2007, 28, 1234-1239. [PDF]
61. Agrafiotis DK*, A. Gibbs, Zhu F, Izrailev S, and E. Martin.
Conformational sampling of bioactive molecules: a comparative study. J.
Chem. Info. Model. 2007, 47, 1067-1086. [PDF]
62. Agrafiotis DK*, Bandyopadhyay, Wegner JD, Van Vlijmen H. Recent advances
in chemoinformatics. J. Chem. Info. Model., 2007, 47,
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63. Zhu F*, Agrafiotis DK. Recursive distance
partitioning algorithm for common pharmacophore identification. J. Chem.
Info. Model. 2007, 47, 1619-1625. [PDF]
64. Agrafiotis DK*, Bandyopadhyay, Carta DG, Knox
AJS, Lloyd DG. 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),
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65. Agrafiotis DK*, Shemanarev M, Connolly PJ, Farnum
M, Lobanov VS. SAR maps: a new SAR visualization technique for medicinal
chemists. J. Med. Chem. 2007, 50(24), 5926-5937. [PDF]
66. Agrafiotis DK*, et al. Advanced Biological and Chemical Discovery
(ABCD): centralizing discovery knowledge in an inherently decentralized world. J.
Chem. Info. Model. 2007, 47, 1999-2014. [PDF]
67. Bandyopadhyay D, Agrafiotis DK*. A self-organizing algorithm for
molecular alignment and pharmacophore development. J. Comput.
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68. Liu P*, Zhu F,
Rassokhin DN, Agrafiotis DK*. A self-organizing algorithm for modeling
protein loops. PLoS Comput. Biol.
2009, 5(8), e1000478. [PDF]
69. Kolpak J, Connolly
PJ, Lobanov VS, Agrafiotis DK*. Enhanced SAR maps: Expanding the data
rendering capabilities of a popular medicinal chemistry tool. J. Chem. Info. Model. 2009, 49, 2221-2230. [DOI]
70. Bonnet P, Agrafiotis
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finding what common search methods miss. J.
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71. G. Tresadern*, and Agrafiotis
DK. Conformational sampling with stochastic proximity embedding (SPE) and
self-organizing superimposition (SOS): Establishing reasonable parameters for
their practical use. J. Chem. Info. Model.
2009, 49, 2786–2800. [DOI]
72. Cepeda MS, Lobanov VS,
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Broadening access to electronic health care databases. Nat. Rev. Drug Discov. 2010, 9, 84. [DOI]
73. Liu P*, Agrafiotis
DK, Theobald DL. Fast determination of the
optimal rotation matrix for weighted superpositions. J. Comput. Chem.
2010, 31, 1561-1563. [DOI]
74. Agrafiotis DK*, Wiener JJM.
Scaffold Explorer: An interactive tool for organizing and mining SAR data
spanning multiple chemotypes. J. Med. Chem. 2010, 53(13), 5002-5011. [DOI]
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Bandyopadhyay D, Liu P. Stochastic proximity embedding: methods and
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76. Liu P*, Agrafiotis
DK, Theobald DL. Reply to comment on: 'Fast
determination of the optimal rotation matrix for macromolecular superpositions’. J. Comput. Chem. 2011,
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77. Tsantili-Kakoulidou A, Agrafiotis DK. Report on the 18-th
European symposium on quantitative structure-activity relationships. Expert Opin. Drug
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78. Agrafiotis DK*, Wiener JJM, Skalkin
A, Kolpak J. Single R-group polymorphisms (SRPs) and R-cliffs: An intuitive
framework for analyzing and visualizing activity cliffs in a single analog
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UNDER REVIEW
80. Liu P*, Agrafiotis
DK, Rassokhin DN. Power keys: a novel class of topological descriptors
based on exhaustive subgraph enumeration and their application in substructure
searching. Submitted.
81. Liu P*, Agrafiotis
DK, Rassokhin DN, Yang E. Accelerating chemical database searching through efficient
manipulation of lossless compressed fingerprints using graphics processing units
(GPUs). Submitted.
1. Agrafiotis DK, Bone R, Salemme FR, Soll R. System and
method for automatically generating chemical compounds with desired properties.
US Patent 5,463,564, October 31, 1995. [USPTO]
2. Agrafiotis DK, Bone R, Salemme FR, Soll R. System and
method for automatically generating chemical compounds with desired properties.
US Patent 5,574,656, November 12, 1996. [USPTO]
3. Agrafiotis DK, Bone R, Salemme FR, Soll R. 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. Agrafiotis DK, Bone R, Salemme FR Soll R. 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. Agrafiotis DK, Salemme FR. Method,
system, and computer program product for representing
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6. Agrafiotis DK, Bone R, Salemme FR, Soll R. System, method
and computer program product
for identifying chemical compounds
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8. Agrafiotis DK,
Lobanov VS, Salemme FR. System, method, and computer program product for
representing proximity data in a multidimensional space. US Patent 6,453,246,
September 17, 2002. [USPTO]
9. Dhanoa DS, Doller D, Meegalla S, Soll R, Agrafiotis
DK, Wisnewski N, Silver GM, Stinchcomb DT, Seward RL. Use of 1,3-substituted
pyrazol-5-yl sulfonates as pesticides". US Patent
6,506,784, January 14, 2003. [USPTO]
10. Meegalla S, Agrafiotis DK, Dhanoa
D, Doller D, Soll R, Wisnewski N, Silver G, Stinchcomb
D, Seward RL, Sha D. 1-aryl-3-thioalkyl pyrazoles, and the synthesis thereof and use thereof as
insecticides. US Patent 6,518,266, February 11, 2003. [USPTO]
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Lobanov VS, Salemme FR. Method, system and computer program product for
nonlinear mapping of multidimensional data. US Patent 6,571,227, May 27, 2003. [USPTO]
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encoding and building products of a virtual combinatorial library. US Patent
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system, and computer program product for determining properties of
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Rassokhin DN, Lobanov VS, Salemme FR. System, method, and computer program
product for representing object relationships in a multidimensional space. US
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16. Agrafiotis DK,
Lobanov VS, Salemme FR. Method, system, and computer program product for
analyzing combinatorial libraries. US Patent 7,054,757, June 13, 2006. [USPTO]
17. Agrafiotis DK,
Lobanov VS, Salemme FR. Method, system and computer program product for
non-linear mapping of multi-dimensional data. US Patent 7,117,187, October 3, 2006. [USPTO]
18. Agrafiotis DK,
Rassokhin DN, Lobanov VS, Salemme FR. 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.