Qiaolin Deng

Work Address

Ag Discovery Research Department
Rohm and Haas Company
727 Norristown Road
Spring House, PA 19477
Tel: (215) 619-5583
Fax: (215) 619-1617
E-mail: Qiaolin_Deng@rohmhaas.com

Home Address

700 Lower State Road, 7C2
North Wales, PA 19454
USA
Tel: (215) 591-5275
E-mail: qiaolin_deng@hotmail.com

Career Objective

Develop and use computational tools for rational drug design and drug discovery.

Education

Ph.D., Chemistry, Peking University, 1994

M.S., Chemistry, Peking University, 1991

B.S., Chemistry, Peking University, 1988

Research Experience

Rohm and Haas BIONET Research Fellow

Protein Modeling on EcR.

Postdoctoral Researcher (Advisor: Professor K. N. Houk)
Protein modeling and ab initio quantum mechanics calculations on transition states to elucidate antibody catalysis. Discovered that Diels-Alder reactions are catalyzed by hydrogen-bonding between transition states and antibody hydrogen-bonding residues; also discovered that the stereoselectivity comes from the specific recognition of one transition state configuration by the antibody.

1994 - 1995, Tsukuba Life Science Center, RIKEN, Japan
Postdoctoral Researcher (Advisor: Dr. Akinori Sarai)
Molecular modeling and bio-informatics. Projects included DNA triplet dynamics simulation and DNA sequence recognition analysis by DNA-binding proteins. Protocol developed to screen the binding site of c-Myb by using systematic binding data.

1991 - 1994, Department of Chemistry, Peking University, China
Research Assistant (Advisors: Professor Youqi Tang and Professor Luhua Lai)
Computer-aided drug design on inhibitors for Phospholipase A2. Work included structure-based inhibitor design, lead compounds optimization, QSAR analysis, synthesis and activity assay.

1988 - 1991, Department of Chemistry, Peking University, China
Research Assistant (Advisor: Professor Xiaojie Xu)
Developed program to apply the simulated annealing method to the conformational analysis of bio-active peptides.

Technical Skills and Expertise

1. Operating system - UNIX, VAX/VMS, Windows, Mac-OS
2. Code Developement - Fortran 77 and C++
3. Computational methods - ab initio and semi-empirical quantum mechanics
4. Protein Modeling - Homology modeling, Molecular Mechanics, Molecular Dynamics, Simulated Annealing, Monte Carlo search and docking
5. QSAR - CoMFA analysis
6. Database Search - CSD, PDB, PIR, GenBank, GCG, BLAST, FASTA
7. Software - Sybyl, Quanta/Charmm, Insight II/Discover, Macromodel, Gaussian, Spartan, Mopac, AbM, Dock, AutoDock

Honors and Awards

Guanghua fellowship for graduate students (1992)
Guanghua fellowship for graduate students (1990)
Outstanding graduating senior (1988)

Professional Affiliations

American Chemical Society (ACS)
American Association for the Advancement of Science (AAAS)

References

References available upon request

Publications

1. Jian Xu, Qiaolin Deng, Jiangang Chen, Kendall. N. Houk, Johannes Bartek, Donald Hilvert, and Ian A. Wilson, Evolution of Shape Complementarity and Catalytic Efficiency from a Primordial Antibody Template, Science, Vol. 286, No. 5448, 2345-2348, 1999.

2. Andreas Heine, Enrico A. Stura, Jari T. Yli-Kauhaluoma, Changuo Gao, Qiaolin Deng, Brett R. Beno, K. N. Houk, Kim D. Janda and Ian A. Wilson, Catalysis of a disfavored reaction: An antibody exo Diels-Alderase-TSA-inhibitor complex at 1.95 Å resolution, Science, Vol. 279, No. 5358, 1934-1940, 1998.

3. Qiaolin Deng, Bert E. Thomas IV, K. N. Houk and Paul Dowd, Transition Structures of the Ene Reactions of Cyclopropene, Journal of the American Chemical Society , Vol. 119, No.29, 6902-6908, 1997.

4. Qiaolin Deng, Shunsuke Ishii and Akinori Sarai, Binding-Site Analysis of c-Myb: Screening of Potential Binding Sites by Using the Mutation Matrix Derived from Systematic Binding Affinity Measurements, Nucleic Acids Research, Vol 24, No. 4, 766-774, 1996.

5. Qiaolin Deng, Bin Cao and Luhua Lai, Receptor mapping by Comparative Molecular Field Analysis of Phospholipase A2 Inhibitors, Journal of the Chinese Chemical Society, Vol. 42, 739-744, 1995.

6.Qiaolin Deng, Bin Cao, Luhua Lai and Youqi Tang, Comparative Molecular Field Analysis (CoMFA) Study on Known Inhibitors of Phospholipase A2, Acta Pharmaceutica Sinica, Vol. 30, No. 6, 428-434, 1995.

7. Zhaowen Luo, Qiaolin Deng, Luhua Lai, Xiaojie Xu and Youqi Tang, Molecular Dynamics Study on Phospholipase A2 and its Complex, Acta Physico-Chimica Sinica, Vol. 11, No. 7, 622-626, 1995.

8. Qiaolin Deng, Luhua Lai, Yu Luo, Yanli Wang, Xiaojie Xu and Youqi Tang, Homology Protein Structure Prediction for Phospholipase A2, Chinese Chemical Letters, Vol. 5, No. 10, 865-868, 1994.

9. Luhua Lai, Leyu Wang, Qiaolin Deng, Yuzhen Han, Libin Ma, Xiaojie Xu, Youqi Tang, Constraint Monte Carlo Simulated Annealing: Application in Peptide Conformational Analysis in Solution, Acta-Chimica Sinica, Vol 10, No. 10, 867-869, 1994.

10. Qiaolin Deng, Luhua Lai, Yuzhen Han, Zhenwei Miao, Aixue Ji and Xiaojie Xu, Application of Simulated Annealing: Study on the Relationship Between Conformation of Linear Peptides and Their Cyclization Yields, Acta Physico-Chimica Sinica, Vol. 10, No. 5, 444-448, 1994.

11. Qiaolin Deng, Luhua Lai and Xiaojie Xu, A Computer Aided Program for Introduction of Engineered Disulfide Bonds, Progress in Biochemistry and Biophysics, Vol. 19, No. 5, 377-380, 1992.

12. Qiaolin Deng, Yuzhen Han, Luhua Lai, Xiaojie Xu, Youqi Tang and Minghong Hao, Application of Monte-Carlo Simulated Annealing on Conformational Analysis, Chinese Chemical Letters, Vol. 2, No.10, 809-812, 1991.

Book

Qiaolin Deng, chapter 6 and chapter 8, Protein Structure Prediction and Molecular Design, ed. Luhua Lai, Peking University Press, Beijing, 1993 (in Chinese).

Conference Papers

1. Qiaolin Deng, K. N. Houk and Donald Hilvert, Theoertical Study of the Diels-Alder Catalytic Antibody 1E9: Catalytic Mechanism and Cross-reactivity with Steroid Binding (DB3) Antibodies, 217th ACS Meeting, Anaheim, 1999.

2. Qiaolin Deng, K. N. Houk, Theoretical Exploration of the Acceleration and Stereoselectivity in Diels-Alder Catalysis by Antibody 39A11, 216th ACS National Meeting, Boston, 1998.

3. Qiaolin Deng, Luhua Lai, Yu Luo, Xiaojie Xu, Inhibitor Design for Human Rheumatoid Arthritic Synovial Fluid Phospholipase A2, IUCr XVI, 163, Beijing, 1993.

4. Leyu Wang, Qiaolin Deng, Luhua Lai, Yuzhen Han, Xiaojie Xu, Constraint Peptide Conformational Analysis by Monte Carlo Simulated Annealing, IUCr XVI, 153, Beijing, 1993.

5. Qiaolin Deng, Luhua Lai, Yuzhen Han, Xiaojie Xu, Conformational Analysis of Dynorphin (1-13), Proceedings of the 1992 Chinese Peptide Symposium, Peptides: Biology and Chemistry, 245-246, ed. Yucang Du, James P. Tam, Youshang Zhang, ESCOM, Leiden, 1992.

6.Yuzhen Han, Qiaolin Deng, Luhua Lai and Xiaojie Xu, Optimization by Simulated Annealing and Studies on Molecular Conformations, Computer Chemistry Monograph Series 2: Selected Papers and Applied Chemistry, Science Press, Beijing, 68-71, 1991.