Consultant in Scientific Computing and Visualization from August 1987 to
present. Current clients include pharmaceutical and chemical companies, computer
manufacturers and government research labs.
Senior Theoretical Chemist at Abbott Laboratories from October 1981 to
August 1987.
Postdoctoral Fellowship at the National Resource for Computation in Chemistry
(NRCC) at the Lawrence Berkeley Laboratory,
University of California at Berkeley from May 1980 to October 1981.
Education
Ph.D. in Physical Chemistry, 1980, from University
of Illinois at Chicago (UIC). Thesis: Molecular Orbital Studies
of Nucleosides and Nucleoside Bases.
M.S. in Chemistry, from UIC, 1976.
B.S. with high honors in Chemistry, from UIC, 1973.
Participated in "Thesis Parts" program at Argonne
National Laboratory, Argonne, Illinois from June 1978 to December 1979.
chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery,
Man-Ling Lee, Ignacio Aliagas, Jianwen A. Feng, Thomas Gabriel, T. J. O’Donnell, Benjamin D. Sellers, Bernd Wiswedel and Alberto Gobbi,
Journal of Cheminformatics, 2017 9:38 doi: 10.1186/s13321-017-0228-9
Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives,
Richard K. Belew, Stefano Forli, David S. Goodsell, T. J. O’Donnell, and Arthur J. Olson,
J Chem Inf Model. 2016 Aug 22;56(8):1597-607. doi: 10.1021/acs.jcim.6b00248
Relational database file can take us beyond the plain text file format, Presentation at CINF 2016 Data Summit - 251st ACS Meeting, March 2016 Slides
Design and Use of Relational Databases in Chemistry, CRC Press, 2009.
Virtual Classrooms and E-Learning: Bringing Cheminformatics Training Into Academic and Industrial Settings,
TJ O'Donnell, Norah E. MacCuish, J. D. MacCuish,
ChemAxon 2005 User Group Meeting Proceedings, Budapest, Hungary, May 19th, 2005
Goodsell, D.S. & O'Donnell, TJ, Displays on Display:
Molecular Graphics Art Show. IEEE Comp. Graph. & Appl. 14(6),
5-6, 1994
A General Approach for Atom-Type Assignment and the Interconversion of
Molecular Structure Files, TJ O'Donnell, et. al., J. Comput. Chem., 12,
209-213 (1991).
Mechanism of inhibition of DNA gyrase by quinolone
antibacterials: a cooperative drug-DNA binding model, Linus L. Shen,
Lester A. Mitscher, Padam N. Sharma, T. J. O'Donnell, Daniel W. T. Chu,
Curt S. Cooper, Terry Rosen, Andre G. Pernet, Biochemistry, 28(9), 3886-3894, 1989
Uses of Computer Graphics in Computer Assisted Drug Design, TJ O'Donnell,
Chapter 1 in Computer Aided Drug Design, T.A. Perun, ed., Marcel Dekker
Inc., New York, 1989.
Computer Graphics Applied to Molecular Modeling, TJ O'Donnell and Cary
Chabalowski, Chapter in New Methods in Drug Research, vol. 2 (1987),
J.R. Prous Science, Barcelona.
TABLES, a program to display space-group symmetry information in three dimensions,
C. Abad-Zapatero and TJ O'Donnell, J. Appl. Cryst., 20, 532-535 (1987)
A 3-Dimensional Docking Device for Molecular Modeling, TJ O'Donnell and
Karl Mitchell, J. Molecular Graphics, 5, 76-79 (1987).
Determining the Structure of a Glycopeptide-Ac2-D-Ala-D-Ala Complex using
NMR Parameters and Molecular Modeling, S. Fesik, TJ O'Donnell, R.T. Gampe
and E.T. Olejniczak, J. Amer. Chem. Soc., 108, 3165-3120 (1986).
Quantum and Molecular Mechanical Studies on Alanyl Dipeptide, S. Weiner,
U.C. Singh, TJ O'Donnell and P.A. Kollman, J. Amer. Chem. Soc., 106,
6234-6245 (1984).
Computer-Assisted Drug Design, Y.C. Martin, K.H. Kim, T.D. Koschmann, TJ
O'Donnell, Proceedings of the VI International Conference on Computers
in Chemical Research and Education (ICCCRE), Washington, D.C., July, 1982.
Some Computational Trends in Theoretical Chemistry, W.A. Lester, Jr., M.
Dupuis, TJ O'Donnell and A.J. Olson, in IUPAC Frontiers of Chemistry,
K.J. Laidler, ed., Pergammon Press, New York, p. 159, 1982.
GRAMPS - A Graphics Language Interpreter for Real-Time, Interactive, Three-Dimensional
Picture Editing and Animation, TJ O'Donnell, A. Olson, Computer Graphics,
15, 133 (1981) also known as Proceedings of SIGGRAPH-ACM, Dallas,
August, 1981.
UV Photoelectron Studies of Volatile Derivatives of Nucleosides, C. Yu,
TJ O'Donnell and P. R. LeBreton, J. Phys. Chem., 85, 3851 (1981).
A 3-dimensional Animated Videocassette on the Unit Cell, C.F. Liu, TJ O'Donnell,
J.I. Gelder and L.L. Jones, J. Chem. Educ., 57, 590 (1980).
Ab-initio Quantum Mechanical Characterization of the Low-Lying Cation
Doublet States of Uracil. Interpretation of UV and X-ray Photoelectron Spectra,
TJ O'Donnell, P. R. LeBreton, J. D. Petke and L. L. Shipman, J. Phys. Chem.,
84, 1975 (1980).
Ab-initio Quantum Mechanical Characterization of the Ground State
of Uracil, TJ O'Donnell, P. R. LeBreton and L. L. Shipman, J. Phys. Chem.,
82, 343 (1978).
UV Photoelectron Studies of Biological Pyrimidines: The Valence Electronic
Structure of Methyl Substituted Uracils, A. Padva, TJ O'Donnell and P. R.
LeBreton, Chem. Phys. Lett., 41, 278 (1976).
designed and implemented gMol molecular modeling system, 2010-2012
designed and implemented MTK molecular modeling system, 1993-94
designed and implemented Abbott's CMD molecular modeling system, 1981-83
wrote GRAMPS graphics and animation language, 1979-81
worked on development of GRASS graphics system, 1973-76
Animations
DNA Structure, part of Indianapolis Children's Museum exhibit, 1993
Tomato Bushy Stunt Virus and ADAM, shown at the SIGGRAPH film
and video show in 1981.
The Hydrogen Atom According to Quantum Mechanics, Cubic Cells, Symmetry
and Mirror Images, and Quantum Mechanical Description of the Hydrogen
Molecule Cation, 1973-78
Exhibitions
Interface: A Juried Exhibition Exploring Art, Science and Technology, California
Center for the Arts, Escondido, CA, March 19, 2002 - June 30, 2002.
Seeing the Unseeable, Reuben H. Fleet Space Theatre, San Diego, CA August,
2000 -
Out of Sight: Imaging/Imagining Science, Santa Barbara Art Museum, Santa
Barbara, CA, April 11-June 7 1998
From Holography to Virtual Photography, Technorama, Winterthur, Switzerland,
August 16, 1996-April 13, 1997
Computed Images, Group Show, Stephen Wagner Studio, Chicago, March 28,
30, 1996
Computed Images, Cafe Avanti, Chicago, December 15 - February 4, 1996
The Role of Computer Graphics Technology in the Human Perception of Reality,
The Martin Luther King, Jr. Performance and Cultural Arts Complex, Columbus,
OH April 1-30, 1995
Museum of Science & Industry, Chicago, IL, February-April 1995
Virtual Photography PHSColograms, Gahlberg Gallery: The Arts Center, College
of DuPage, DuPage, IL, November 25 - December 20, 1994