Waiting for funding
A postdoctoral position may soon be available in
the Molecular Biology department at The Scripps
Research Institute in La Jolla, California in
the laboratory of Dr. Victoria A. Roberts.
The research involves the continuing development
and application of the intermolecular docking program DOT.
DOT performs an exhaustive search of all orientations
of one molecule about another, calculating the energy for
This calculation provides not only the best energy docked orientations
but also shows pathways of approach for the two molecules.
The size of the calculation is not directly dependent
on the size of the molecules,
making it suitable for examining interactions between
large molecules such as proteins.
Currently, interactions between electron-transfer proteins and
between DNA repair enzymes and inhibitors and DNA are
DOT is described in the
Proceedings of the 1995 ACM/IEEE Supercomputing Conference
Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi,
V., Mitchell, J. C., Nelson, E., Tsigelny, I., and Ten Eyck, L. F.,
"Protein Docking Using Continuum Electrostatics and Geometric Fit"
Prot. Eng., 14, 105-113.
An application to predicting the complex of two electron-transfer proteins is
Roberts, V. A. and Pique, M. E., (1999)
"Definition of the Interaction Domain for
Cytochrome c on Cytochrome c Oxidase:
III. Prediction of the Docked Complex by a Complete, Systematic Search",
J. Biol. Chem., 274, 38051--38060.
The candidate should have a Ph.D. degree
in biochemistry or chemistry.
Experience with analysis or modeling of protein structures and
with the UNIX operating system is highly desirable.
Familiarity with the C programming language will be helpful.
Candidates should be interested in learning the
sophisticated computer graphics programs
that are required to analyze DOT results.
Interested candidates should send applications containing a
full CV, a one-page summary of research experience, and full
addresses plus telephone numbers of three references to:
Victoria A. Roberts
Department of Molecular Biology, MB4
The Scripps Research Insitute
10550 North Torrey Pines Road
La Jolla, CA 92037