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David F. Green
Associate Professor and Graduate Program Director
Department of Applied Mathematics and Statistics
Stony Brook University
Math Tower, Room P-137
Stony Brook, NY 11794-3600, USA
Office: +1-631-632-9344
Fax: +1-631-632-8490
dfgreen@stonybrook.edu
http://www.ams.sunysb.edu/~dfgreen/
Massachusetts Institute of Technology
Cambridge, MA 02139, USA
Sept. 1997 – Sept. 2002
Doctor of Philosophy in Biological Chemistry
Thesis Supervisor: Prof. Bruce Tidor
Thesis Title: Optimization of Electrostatic Binding Free Energy: Applications to the Analysis and Design of Ligand Binding in Protein Complexes.
Simon Fraser University
Burnaby, BC V5A 1S6, Canada
Sept. 1993 – June 1997
Bachelor of Science in Chemistry (Honors)
Minor in English Literature
| 2010 | Stony Brook Applied Math \& Statistics Outstanding Teacher Award |
| 2007 | Microsoft Research Computational Challenges in Synthetic Biology Award |
| 2003 | MIT $50K Entrepreneurship Competition – Finalist (MolySym, Inc.) |
| 2001 | Protein Society Symposium – Eli Lilly & Co. Poster Award |
| 1998– 2000 | Merck– MIT Graduate Fellowship in Bioinformatics |
| 1997 | Hypercube Award for Molecular Modeling & Computational Chemistry |
| 1996 | Canadian Society of Chemical Industry Merit Award |
| 1993– 1997 | The Simon Fraser Entrance Scholarship |
| 1993 | British Columbia Provincial Examination Gold Medal |
Stony Brook University (State University of New York
Department of Applied Mathematics and Statistics
Sept. 2011 – present
Associate Professor
May 2011 – present
Graduate Program Director
Sept. 2005 – Aug. 2011
Assistant Professor
Development and application of novel methods for the computational study of carbohydrates and glycoproteins. Application of computational approaches to the study of specificity in protein--protein interactions. Development and application of methods for protein interface design.
Massachusetts Institute of Technology
Biological Engineering Division
Computer Science and Artificial Intelligence Laboratory
Sept. 2002 – Aug. 2005
Postdoctoral Associate
Development of improved methods for discrete conformational search
in protein design applications. Computational design of a
protein–peptide binding system for use as a fMRI contrast agent.
Development and integration of ligand design software into commercial
applications.
Massachusetts Institute of Technology
Department of Chemistry
Nov. 1997 – Aug. 2002
Graduate Research Assistant — Laboratory of Prof. Bruce Tidor
Development and application of continuum electrostatic methods
for the analysis and design of ligands for protein targets. Development
of ligand design tools based on electrostatic optimization.
Simon Fraser University
Department of Chemistry
May – Dec. 1996
Undergraduate Research Assistant — Laboratory of Prof. B. Mario Pinto
Computational analysis of the conformational preferences of peptide mimics of carbohydrates.
Simon Fraser University
Department of Chemistry
May – Aug. 1995
Undergraduate Research Assistant — Laboratory of Prof. Roland K. Pomeroy
Synthesis and characterization of Group VIII transitional metal complexes containing dative metal–metal bonds.
Simon Fraser University
Department of Chemistry
May – Aug. 1994
Undergraduate Research Assistant — Laboratory of Prof. B. Mario Pinto
NMR studies of the configurational equilibria of N-arylglucopyranosylamines and N-aryl-cyclohexylamines — solvent and substituent effects.
Advisory Positions
MolySym, Inc. (Cambridge, MA, USA)
Sept. 2005 – present
Scientific Advisor
Nov. 2002 – Oct. 2009
Board Member
Nov. 2002 – Aug. 2005
Chief Software Engineer
Founding member of a small company developing novel physical interfaces for computer-
based molecular modeling.
Delta Search Labs, Inc. (Cambridge, MA, USA)
Sep. 2003 – Mar. 2005
External scientific consultant
Consulting on applications in computational drug design and optimization.
New York Times, Inc. (New York, NY, USA)
Feb. 2003; Mar. 2004
External contract for scientific graphic design
Design and creation of images and graphics for "Science Times."
Stony Brook University
Spring, 2007 – 2009
Topics in Information and Technology Studies (ITS 102)
Spring, 2009 – present
Mathematical Biology (AMS 333)
Fall, 2005 – 2010
Analytical Methods for Applied Mathematics and Statistics (AMS 510)
Spring, 2006 – present
Numerical Methods and Algorithms in Computational Biology (AMS 533)
Massachusetts Institute of Technology
Feb. – May 2004
Teaching Assistant — Foundations of Algorithms and Computational Techniques in Systems Biology (6.971/BE.949J)
Feb. – May 1998
Teaching Assistant — Organic Chemistry I (5.12)
Sept. – Dec. 1997
Teaching Assistant — Laboratory Chemistry (5.310)
Massachusetts Institute of Technology
Feb. – May 1999
Teacher Training — Teaching College-level Chemistry (5.95)
Society Affiliations
| Protein Society: Member | 1999 – present |
| American Chemical Society: Member | 2000 – present |
| Biophysical Society: Member | 2007 – present |
| Biophysical Society: Molecular Biophysics Subgroup Chair | 2009 – 2010 |
Research Articles
1. V. Patsalo, D. P. Raleigh, and D. F. Green.
"Rational and computational stabilization of stabilized variants of Cyanovirin-N that retain affinity and specificity for glycan ligands."
Biochemistry 50 (49): 10698-10712 (2011).
2. D. F. Green.
"A statistical framework for hierarchical methods in molecular simulation and design."
J. Chem. Theory Comput. 6 (5): 1682-1697 (2010).
3. N. Carrascal and D. F. Green.
"Energetic decomposition with the generalized-Born and Poisson-Boltzmann solvent models: Lessons from association of G-protein components."
J. Phys. Chem. B 114 (15): 5096-5116 (2010).
4. H. Taskent-Sezgin, J. Chung, V. Patsalo, S. J. Miyake-Stoner, A. M. Miller, S. H. Brewer, R. A. Mehl, D. F. Green, D. P. Raleigh and I. Carrico.
"Interpretation of p-cyanophenylalanine fluorescence in proteins in terms of solvent exposure and contribution of side-chain quenchers: A combined fluorescence, IR and molecular dynamics study."
Biochemistry 48 (38): 9040-9046 (2009).
5. Y. K. Fujimoto, R. N. TerBush and D. F. Green.
"Computational models explain the oligosaccharide specificity of cyanovirin-N."
Protein Sci." 17 (11):> 2008-2014 (2008).
6. D. F. Green.
"Optimized radii for continuum solvation calculations with carbohydrates."
J. Phys. Chem. B 112 (16): 5238-5249 (2008).
7. D. F. Green, A. T. Dennis, P. S. Fam, B. Tidor and A. Jasanoff.
"Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide."
Biochemistry 45 (41): 12547-12557 (2006).
doi:10.1021/bi060857u
8. D. F. Green and B. Tidor.
"Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface."
Proteins: Struct. Func. Bioinf. 60 (4): 644-657 (2005).
doi:10.1002/prot.20540
9. B. A. Joughin, D. F. Green and B. Tidor.
"Action-at-a-distance interactions enhance protein binding affinity."
Protein Sci. 14 (5): 1363-1369 (2005).
doi:10.1110/ps.041283105
10. D. F. Green and B. Tidor.
"Eschericia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates."
J. Mol. Biol. 342 (2): 435-452 (2004).
doi:10.1016/j.jmb.2004.06.087
11. C. Mattos, J. D. Cohen, D. F. Green, B. Tidor and M. Karplus.
"X-ray structural and simu-lation analysis of protein mutants: R96H in T4 lysozyme."
Proteins: Struct. Func. Bioinf. 55 (3): 733-742 (2004).
doi:10.1002/prot.20031
12. D. F. Green and B. Tidor.
"A comprehensive evaluation of ab initio charge determination methods for use in continuum electrostatic calculations."
J. Phys. Chem. B. 107 (37): 10261-10273 (2003).
doi:10.1021/jp0350971
13. F. Jiang, H. A. Jenkins, D. F. Green, G. P. A. Yap and R. K. Pomeroy.
"A novel metal-chain extension reaction: synthesis of (X)[ Os( CO) 3 (CNBut)] n Mn( CO) 5 (X = Cl, Br, I; n = 1, 2, 3)."
Can. J. Chem 80 (3): 281-291 (2002).
doi:10.1139/v02-016
14. R. J. Batchelor, D. F. Green, B. D. Johnston, B. O. Patrick and B. M. Pinto.
"Conformational preferences in glycosylamines. Implications for the exo-anomeric effect."
Carbohyd. Res. 330 (3): 421-426 (2001).
doi:10.1016/S0008-6215(00)00304-9
15. K. D. Randell, B. D. Johnston, D. F. Green and B. M. Pinto.
"Is there a generalized reverse anomeric effect? Substituent and solvent effects on the configurational equilibria of neutral and protonated N-arylglucopyranosylamines and N-aryl-5-thioglucopyranosylamines."
J. Org. Chem. 65 (1): 220-226 (2000).
doi:10.1021/jo991520j
Book Chapters and Invited Articles
1. D. F. Green.
"Computer graphics, homology modeling, and bioinformatics."
Protein Engineering and Design." (S. Park and J. Cochran, Eds.) CRC Press (2010).
2. D. F. Green and B. Tidor.
"Evaluation of electrostatic interactions."
Current Protocols in Bioinformatics, Unit 8.3 (A. D. Baxevanis et al., Eds.) John Wiley & Sons, Inc. (2003).
doi:10.1002/0471250953.bi0803s02
Patents
1. B. H. Sherman, D. F. Green and K. H. Ruping.
"Method and system for interactive molecular docking and feedback."
US patent pending approval. Filed 06/10/2004 (Provisional 06/10/2003), Appl. No.
2005/0055187 A1.
2. B. H. Sherman, D. F. Green and K. H. Ruping.
"Apparatus and method for integrating a physical molecular model with a computer-based visualization and simulation model."
US patent No. 7,558,707..
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