RAJA DEY, M. Sc., M. Phil., Ph. D.

University of Southern California, Department of Molecular and Computational
Biology, Room 216, Los Angeles, CA 90089. Office Phone: 213 8214280
E mail : rdey@usc.edu & deyraja1@yahoo.co.in
Home Add: 949 W. Adams Blvd. Appt.- 7, Los Angeles, CA 90007,
Home Phone: 213 7495748

University Education

o Ph. D. in Physics (2002), Calcutta University, India
Title of the thesis : Studies on crystal and Molecular Structure of some Organic
Compounds by X-ray Crystallography and Computer Modelling
o Diploma in Micro computer and its application (1993). Jadavpur University _
Grade A
o M. Phil. in Environmental Science (1992), Jadavpur University, India. Title of the thesis : Atmospheric boundary layer and role of convection -
First Class
o Degree in Education(1991), Calcutta University, India - First Class
o M. Sc. in Physics (1988), Calcutta University, India - First class,
[ special paper _ x-rays and crystallography ]
o B. Sc. Honours in Physics (1985), Calcutta University, India.

Postdoctoral experience

o NIH fellowship: 1st Jan, 2006 - continuing
Research Associate: Dept. of Mol. and Comp. Biol., University of Southern California, Los Angeles, CA 90089 and Crystol Chemistry,
Dept. of Chemistry and Biochemistry, Colorado University at Boulder
The same group moved from Boulder to Los Angeles in June, 2006.
o Carl Trigger Foundation fellowship: 2003 - 2005
Postdoctoral research: Chalmers University of Technology, Department of
Chemistry and Bioscience, Box 462, 40530 Goteborg, Sweden

Research Experience

(1997 - 2002)
o X-ray crystal structure determination of small molecules of biological importance ( steroid hormones being the main area of research ).
o Homology modelling, Ligand docking and study of ligand-protein interaction ( thrust area
of research: steroid receptors and corticosteroid binding globulins ).

(2002 - 2003)
o Molecular dynamics simulation ( thrust area: relative binding of different corticosteroids to corticosteroid binding globulin ).
o Different modules of Insight II have been used for modelling study.

(2003 - 2004)
o Acquired experience of data collection using MAR-CCD, ADSC-CCD detectors at Lund, Sweden; at ESRF, Grenoble, France.
o Experience of working with Mosflm, CCP4, CNS and O programs. Got first time hands on experience of solving two protein structures.
(Mycobacterium tuberculosis chorismate mutase with/without inhibitor).
o Some experience of crystallization by hanging drop method. Crystals are obtained for a mutant Bacillus Subtilis chorismate mutase.
o Some experience of preparing isomorphous heavy atom derivative.

(2005)
1. 1 point advanced graduate course in 'Practical Protein Crystallization', 7th February to
11th February, 2005, BMC, Uppsala, Sweden.
2. 1 point Ph. D. course in 'Introduction Biomolecular NMR Spectroscopy', 24th January to
28th January, 2005, Swedish NMR Centre, Goteborg University, Sweden.
* Worked on small molecule crystals of 25 different compounds, collected data using our in-house SMART CCD detector, integrated by SAINT,
absorption correction by SADABS, solved the structures by XPREP, XS and XP and finally refined by XL.

Current research

Trying to crystallize HIV-1 IN core and human APE1 with/without inhibitors.
Recently acquired experience of virtual screening and docking using a large small molecule data base. Some experience of working in structure based and ligand based drug design using trial version of ICM 3.4-8f and Discovery Studio 1.7. Some experience of using DOC 6, Modeller.
Acquired experience of using HKL2000, SHARP and solved known protein-dna complex from sad data as a trial basis.
Recently solved an unknown multiprotein-dna complex at 3.6A. Now in the process of refinement.

List of Publications :

1998 - 2007

1 .Raja Dey, A. Pal, A. Bera, B. P. Mukhopadhyay, A. Banerjee; Crystal structure of 1,2,3,7-tetramethoxy-5,6-phenanthraquinone,
C18H16O6;Z. Kristallogr. NCS 213 (1998) 491-492
2. Raja Dey, A. Banerjee; Structure of N,N,N-trimethyl-triazole-2,4,6-trione; Indian J. Phys. 73A(4), 543-551 (1999).
3. Raja Dey, S. Roychowdhury, P. Roychowdhury, L. Righi; Structure of de-oxy corticosterone-21-hemisuccinate;
Journal of Chemical Crystallography, Vol. 29, No. 12, 1999, pp 1265-69.
4. Raja Dey, S. Roychowdhury, P. Roychowdhury, L. Righi; Structure of de-oxy corticosterone (4-pregnen-21-ol-3,20-dione);
Journal of Chemical Crystallography, Vol.29, No. 12, 1999, pp 1271-75.
5. Raja Dey, P. Roychowdhury, C. Mukharjee; Homology modelling of the ligand-binding domain of glucocorticoid receptor: binding site
interactions with cortisol and corticosterone; Protein Engineering, Vol. 14 no. 8 pp. 565-571, 2001.
6. Raja Dey and P. Roychowdhury; Homology modelling of the ligand binding domain of mineralocorticoid receptor: close structural kinship
with the ligand binding domain of glucocorticoid receptor and their similar binding mode with DOC (de-oxy corticosterone);
Journal of Biomolecular Structure and Dynamics, Vol. 20, No. 1, pp. 21-29, 2002.
7. Raja Dey and P. Roychowdhury; Homology model of rabbit corticosteroid binding globulin: binding site interactions with corticosteroids -
6th European conference on Rheology “eurheo 2002”.
8. Raja Dey, T. Banerjee, P. Roychowdhury, S Chaudhuri; X-ray elucidation of 17_-pregna- 2,4-dien-20-yne-(2,3-d) isoxazole-17_-ol;
Journal of Chemical Crystallography, Vol. 31(5), pp. 263-266, 2001.
9. Rahul Bhattacharya, Mau Sinha Roy, Raja Dey, Lara Righi, Gabriele Bocelli and Asutosh Ghosh; Synthesis, crystal structure and
thermochromism of benzimidazolium tetrachlorocuprate : (C7H7N2)2 [CuCl4]; Polyhedron, Vol. 21, pp. 2561-2565, 2002.
10. Raja Dey and P. Roychowdhury; Homology model of human corticosteroid binding globulin : a study of its steroid binding ability and a plausible
mechanism of steroid hormone release at the site of inflammation; Journal of Molecular Modelling, Vol. 9, pp. 183-189, 2003.
11. Rahul Bhattacharya, Sumana Chanda, Raja Dey and Asutosh Ghosh; Synthesis and Crystal structure of Bis (2- aminopyridinium)
Tetrachlorocuprate(II); Journal Of Indian Chemical Society, 81, No. 1, pp 18, (2004).
12. Raja Dey, Vratislav Langer, P. Roychowdhury, S. Roychowdhury and M. G. B. Drew 21-
deoxycortisone (17-hydroxy-4-pregnene-3,11,20-trione); Acta Cryst C61, o201-o203 (2005).
13. Raja Dey, Sumana Chanda, Ajit Pal, S. Roychowdhury; 21-acetoxy-17_ -4-pregnene-
3,20-dione, Acta Cryst E61, o980-o982, (2005).
14. Raja Dey, Kakoli Mukharjee, Vratislav Langer, and P. Roychowdhury, A titanium
salicylate, Na4[Ti(C7H4O3)3]2.11H2O; Acta Cryst E61, m1495-m1497 (2005).
15. Raja Dey, Tapati Banerjee, Vratislav Langer, Sibdas Ray and P. Roychowdhury, 5-
amino-1-benzyl-4-cyano-3-methylimidazolium toluene-p-sulfonate; Acta Cryst E61,o4039-o4041 (2005).
16. Mats Ökvist, Raja Dey, Severin Sasso, Peter Kast & Ute Krengel; 1.6 Å crystal structure of the secreted chorismate mutase from
Mycobacterium tuberculosis: Novel fold topology revealed. JMB, 357, 1483-1499 ( Joint 1st authorship)
17. Raja Dey, Tapati Banerjee, Vratislav Langer, Sibdas Roy and Priyobroto Roychowdhury; 5-amino-1-[2-(diethylamino)ethyl]-1H-
imidazole-4-carboxamide; Acta Cryst. E62, o814-o816(2006).
18. Ute Krengel, Raja Dey, Mats Ökvist, Severin Sasso, & Peter Kast; Preliminary X-ray crystallographic analysis of the secreted chorismate
mutase from Mycobacterium tuberculosis: a tricky crystallization problem solved. Acta Cryst. F62, 1-5, 2006.
19. Morsy A. M. Abu-Youssef, Raja Dey, Yousry Gohar, Alshima'a
A. Massoud, Lars Ohrstrom, Vratislav Langer, Synthesis and structure of silver complexes with nicotinate type ligands having antibacterial
activities against clinically isolated antibiotic resistant pathogens, Journal of Organic Chemistry, 2007.

Reports of International Conferences and workshops:

1. Raja Dey and P. Roychowdhury; Homology modeling of the ligand binding domain of glucocorticoid receptor complexed to the X-ray structure
of three glucocorticoids, Birth Centenary Celebration of Prof. K. Banerjee, SYMPOSIUM ON RECENT TRENDS IN
CRYSTALLOGRAPHY AND ITS APPLICATION, September, 15-16, 2000, Indian Association for the Cultivation of Science, Jadavpur,
Calcutta 700 032, India.
2. Raja Dey and P. Roychowdhury; Homology model of rabbit corticosteroid binding globulin: binding site interactions
with corticosteroids - Oral presentation - 6th European conference on Rheology “eurheo 2002”.
3. Raja Dey and P. Roychowdhury; Homology modelling of human corticosteroid binding globulin: binding site interactions with cortisol and
aldosterone. - Fourth major international bioinformatics meeting ( SocBiN - Scandinavia ) - April 4, 2002 to April 7, 2002.
4. Raja Dey and P. Roychowdhury; Effect of stereospecific ligand binding on transactivation. Fourth major international bioinformatics meeting
( SocBiN - Scandinavia ) - April 4, 2002 to April 7, 2002.
5. Debjani Roy and Raja Dey; Molecular Dynamics Simulations of Myoglobin in complex with Chlorpromazine in a 8 angstrom water layer.
International Seminar on FRONTIERS OF BASIC & APPLIED MOLECULAR BIOLOGY, Calcutta, India. January 9-11, 2003.
6. Raja Dey and P. Roychowdhury; Homology model of human corticosteroid binding globulin: a study of its steroid binding ability
and a plausible mechanism of steroid hormone release at the site of inflammation. International Seminar on FRONTIERS OF BASIC &
APPLIED MOLECULAR BIOLOGY, Calcutta, India. January 9-11, 2003
7. Raja dey and P. Roychowdhury; A model based study on the effect of stereospecific ligand binding on transactivation. International Seminar
on FRONTIERS OF BASIC & APPLIED MOLECULAR BIOLOGY, Calcutta, India. January 9-11, 2003.
8. Raja Dey and P. Roychowdhury; Homology model of the DNA binding domain of mineralocorticoid receptor: binding interaction
with a non- consensus hormone response element of DNA and study of DNA-induced homodimerization. ICMSB,
Vienna 3-7 September 2003.
9. Participated the SBNet conference at Tällberg, Sweden June 11 - 14, 2004.
10. Raja Dey, Mats Ökvist, Severin Sasso, Peter Kast and Ute Krengel; Structure/Function Studies of Chorismate Mutases. International
conference on 'Structural Biology at Crossroads: From Biological Molecules to Biological Systems', EMBL-Hamburg, Germany,
15th to 18th September, 2004.
11. Mats Ökvist, Raja Dey, Severin Sasso, Peter Kast and Ute Krengel; Structural Investigations of chorismate mutases.
'3rd Norwegian User Meeting - Application of Synchrotron Radiation', Bårdshaug Herregård, Orkanger, Norway, March 10 - 11, 2005.
12. Ökvist, Mats; Krengel, Ute; Grahn, Elin; Dey, Raja; Kast, Peter; Sasso, Severin. Secreted chorismate mutase from Mycobacterium
tuberculosis - a potential virulence factor [Vitenskapelig foredrag]. Tenth Annual Conference of the Swedish Structural Biology Network;
16.06.2006 - 19.06.2006
13. Attended Molsoft ICM Workshop “Protein Structure and Drug Discovery” September 21st to 22nd 2006, La Jolla, CA, USA.
14. Attended SimBioSys - Sun: Luncheon Seminar on Docking, Jan 18, 2007, Tutto Mare Ristorante, 4365 Executive Dr. San Diego, CA, 92121.