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Department of Chemistry and Chemical Biology at Rensselaer Chemistry and Chemical Biology
Curt M. Breneman
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Curt M. Breneman

Professor and Department Head, Department of Chemistry and Chemical Biology
Director, Rensselaer Exploratory Center for Cheminformatics Research
Rensselaer Polytechnic Institute

Ph.D., Organic Chemistry, with High Honors, the University of California, Santa Barbara, 1987
B.S., Chemistry, University of California, Los Angeles, 1980

Career Highlights:
Breneman has presented over 85 academic papers and lectures, published eight book chapters, and received over $10 million in research funding. Throughout his career, he has served as a consultant to several companies including Eastman Kodak Company, Millennium Pharmaceuticals, Concurrent Pharmaceuticals, ICAGEN Pharmaceuticals, and General Electric Co. He has also given invited talks at GE’s Global Research Center, the Nalco-Exxon Technology Symposium, SmithKline Beecham Pharmaceuticals, and Cubist Pharmaceuticals.

An active contributor to the American Chemical Society (ACS), Breneman recently was re-elected Treasurer and Executive Committee Member of the ACS Division of Computers in Chemistry (COMP). He is also serving as the COMP Division fundraising coordinator. Through this role, he originated and administered the CCG Excellence Award, which funds graduate students’ travel to national ACS meetings that is funded by the Chemical Computing Group, Inc. His other professional society memberships include the American Association for the Advancement of Science, the New York Academy of Science, and the International Quantitative Structure Activity Relationship (QSAR) Society.

Breneman has served on the National Institutes of Health’s Molecular, Cellular, and Developmental Neuroscience (MDCN) review panel since 1998. He has reviewed National Science Foundation (NSF) equipment and research proposals since 1991 and ACS Petroleum Research Fund proposals since 1990; he is a permanent member of California’s Tobacco-Related Disease Research Program (TRDRP) review panel. Breneman’s honors include the Best Paper Award at the 1999 Institute of Electrical and Electronics Engineers’ (IEEE) Midnight-Sun Workshop on Soft Computing Methods in Industrial Applications held in Kuusamo, Finland. He also earned a Lilly Endowment Teaching Fellowship in 1991.

Before joining the Rensselaer faculty in 1989, Breneman was a postdoctoral research associate at Yale University. He was granted tenure in 1996 and named Full Professor in 2002. In 2011, he was named an American Chemical Society Fellow for his outstanding achievements in and contributions to cheminformatics and computational chemistry.

Research Areas:
Breneman’s research focuses on understanding and modeling the relationships that exist between molecular structure and function. The highlight of his research is his invention of an entirely new kind of molecular modeling called the Transferable Atom Equivalent (TAE) method. The TAE method allows accurate reconstruction of electron density distributions for very large numbers of drug-sized molecules, or for a few very large protein-sized molecules in a short time frame. Small molecule electron densities can be reconstructed with great speed, enabling large databases to be scanned for desirable combinations of electronic properties in a short period of time. The results of the reconstruction efforts yield sets of electron density-derived molecular property descriptors, as well as atom-centered multipolar representations of molecular electrostatic potential fields.

His team’s work in TAE modeling has received international attention from research groups and pharmaceutical companies, and is being developed through contributions from the NSF, GE, Millennium Pharmaceuticals, ICAGEN Pharmaceuticals, Pfizer Global Research and the Eastman Kodak Company. Breneman’s group is now applying TAE to problems in large and small molecule binding, protein binding site selectivity, and drug design QSAR modeling. Since the TAE method has allowed the development of an entirely new kind of QSAR/QSPR electronic property descriptors, researchers are exploring the application of these indicators for producing accurate statistical models for many classes of intermolecular interactions. Preliminary results on High Performance Liquid Chromatography (HPLC) capacity factors suggest that the new electronic property indicators are highly correlated with specific modes of molecular binding, and should prove to be of general use in QSAR/QSPR work.

Breneman’s researchers also were the first to reconcile the controversial issue of how the atomic charges derived from density partitioning are related to the more familiar electrostatic potential-derived charges. In addition, through the use of electron density partitioning methods, they were the first to show that the conformational preferences of sulfonamides were controlled by the same redistribution of charge and electronic kinetic energy that governs amide stability.

Selected Publications:

Journal Articles:

Zaretzki, J.; Bergeron, C.; Rydberg, P.; Huang, T.-w.; Bennett, K. P.; Breneman, C. M. "Rs-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to Cyp 3a4" J. Chem. Inf. Model. 2011, 51, 1667-1689.

Das, S.; Krein, M. P.; Breneman, C. M. "Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures" J. Chem. Inf. Model. 2010, 50, 298-308.

Das, S.; Krein, M. P.; Breneman, C. M. "Pesdserv: A Server for High-Throughput Comparison of Protein Binding Site Surfaces" Bioinformatics 2010, 26, 1913-1914.

Morrison, C. J.; Breneman, C. M.; Moore, J. A.; Cramer, S. M. "Evaluation of Chemically Selective Displacer Analogues for Protein Purification" Anal. Chem. 2009, 81, 6186-6194.

Das, S.; Kokardekar, A.; Breneman, C. M. "Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions" J. Chem. Inf. Model. 2009, 49, 2863-2872.

Sukumar, N.; Krein, M.; Breneman, C. M. "Bioinformatics and Cheminformatics: Where Do the Twain Meet?" Curr. Opin. Drug Discovery Dev. 2008, 11, 311-319.

Yang, T.; Sundling, M. C.; Freed, A. S.; Breneman, C. M.; Cramer, S. M. "Prediction of Ph-Dependent Chromatographic Behavior in Ion-Exchange Systems" Anal. Chem. 2007, 79, 8927-8939.

Yang, T.; Breneman, C. M.; Cramer, S. M. "Investigation of Multi-Modal High-Salt Binding Ion-Exchange Chromatography Using Quantitative Structure-Property Relationship Modeling" J. Chromatogr. A 2007, 1175, 96-105.

Chen, J.; Yang, T.; Luo, Q.; Breneman, C. M.; Cramer, S. M. "Investigation of Protein Retention in Hydrophobic Interaction Chromatographic (Hic) Systems Using the Preferential Interaction Theory and Quantitative Structure Property Relationship Models" React. Funct. Polym. 2007, 67, 1561-1569.

Chen, J.; Luo, Q.; Breneman, C. M.; Cramer, S. M. "Classification of Protein Adsorption and Recovery at Low Salt Conditions in Hydrophobic Interaction Chromatographic Systems" J. Chromatogr. A 2007, 1139, 236-246.

Liu, J.; Yang, T.; Ladiwala, A.; Cramer, S. M.; Breneman, C. M. "High Throughput Determination and Qser Modeling of Displacer Dc-50 Values for Ion Exchange Systems" Sep. Sci. Technol. 2006, 41, 3079-3107.

Ladiwala, A.; Xia, F.; Luo, Q. O.; Breneman, C. M.; Cramer, S. M. "Investigation of Protein Retention and Selectivity in Hic Systems Using Quantitative Structure Retention Relationship Models" Biotechnol. Bioeng. 2006, 93, 836-850.

Rege, K.; Ladiwala, A.; Hu, S. H.; Breneman, C. M.; Dordick, J. S.; Cramer, S. M. "Investigation of DNA-Binding Properties of an Aminoglycoside-Polyamine Library Using Quantitative Structure-Activity Relationship (Qsar) Models" J. Chem. Inf. Model. 2005, 45, 1854-1863.

Ladiwala, A.; Rege, K.; Breneman, C. M.; Cramer, S. M. "A Priori Prediction of Adsorption Isotherm Parameters and Chromatographic Behavior in Ion-Exchange Systems" PNAS 2005, 102, 11710-11715.

Book Chapters:

A. Ladiwala, C.M. Breneman*, S.M. Cramer*, "Prediction of Chromatographic Separations from Protein Structure Data," in Process-Scale Bioseparations for the Biopharmaceutical Industry ed. A. Shukla, M. Etzel, S. Gadam, CRC Press, (2007).

N. Sukumar and C.M. Breneman*, "QTAIM in Drug Discovery and Protein Modeling" in "The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design" C.F. Matta and R.J. Boyd, Editors. Wiley-VCH (2006)

C.M. Sundling, N. Sukumar, H. Zhang, M.J. Embrechts and C.M. Breneman*, "Wavelets in Chemistry and Cheminformatics," in Reviews in Computational Chemistry, K. Lipkowitz, Ed. Wiley-VCH (2006), 22 295-329. (Invited, peer reviewed)


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