RECCR Rensselaer Exploratory Center for Cheminformatics Research
Rensselaer Exploratory Center for Cheminformatics Research (RECCR)

Publications

News Members Projects Publications Software Data MLI ECCRS

Curt Breneman

N. Sukumar, Michael Krein, Qiong Luo and Curt Breneman, "MQSPR modeling in materials informatics: a way to shorten design cycles?" J. Mater. Sci., DOI: 10.1007/s10853-012-6639-0 (2012).

Margaret R. McLellan, M. Dominic Ryan, and Curt M. Breneman, "Rank Order Entropy: Why One Metric Is Not Enough" J. Chem. Inf. Model., in press (2011). DOI: 10.1021/ci200170k

Jed Zaretzki, Charles Bergeron, Patrik Rydberg, Tao-wei Huang, Kristin P. Bennett, and Curt M. Breneman, "RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4" J. Chem. Inf. Model., 51 (7), 1667–1689 (2011). DOI: 10.1021/ci2000488

Patrik Rydberg, David E. Gloriam, Jed Zaretzki, Curt Breneman and Lars Olsen, "SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism" ACS Med. Chem. Lett., 1, 96-100 (2010).

Sourav Das, Michael P. Krein & Curt M. Breneman, "Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures" J. Chem. Inf. Model., 50 (2), 298–308 (2010). DOI: 10.1021/ci9004139

Sourav Das, Arshad Kokardekar & Curt M. Breneman, "Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions" J. Chem. Inf. Model., 49 (12), 2863–2872 (2009). DOI: 10.1021/ci900317x

N. Sukumar, Michael Krein and Curt M. Breneman, "Bio- and Chem-Informatics: Where do the twain meet?" Curr. Opinion Drug Disc. Devel. 11(3) 311-319 (May 2008)

N. Sukumar & Curt 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 & R.J. Boyd, Editors (Wiley-VCH, 2007), 471-498.

C. Bergeron, T. Hepburn, M. Sundling, N. Sukumar, W. P. Katt, K. P. Bennett, C. M. Breneman, Prediction of peptide bonding affinity: Kernel methods for nonlinear modeling"

Chen, Jie; Luo, Qiong; Breneman, Curt M.; Cramer, Steven M. Classification of protein adsorption and recovery at low salt conditions in hydrophobic interaction chromatographic systems. Journal of Chromatography, A (2007), 1139(2), 236-246.

Ladiwala, Asif; Breneman, Curt M.; Cramer, Steven M. A priori prediction of chromatographic separations from protein structure data. Biotechnology and Bioprocessing (2007), 31(Process Scale Bioseparations for the Biopharmaceutical Industry), 245-275.

Liu, Jia; Yang, Ting; Ladiwala, Asif; Cramer, Steven M.; Breneman, Curtis M.. High throughput determination and QSER modeling of displacer DC-50 values for ion exchange systems. Separation Science and Technology (2006), 41(14), 3079-3107.

Ladiwala, Asif; Xia, Fang; Luo, Qiong; Breneman, Curt M.; Cramer, Steven M.. Investigation of protein retention and selectivity in HIC systems using quantitative structure retention relationship models. Biotechnology and Bioengineering (2006), 93(5), 836-850. CODEN: BIBIAU ISSN:0006-3592. AN 2006:325787

C. Matthew Sundling; N. Sukumar; Hongmei Zhang; Mark J. Embrechts; Curt M. Breneman, "Wavelets in chemistry and cheminformatics." Reviews in Computational Chemistry (2006), 22 295-329. CODEN: RCCHEY ISSN:1069-3599. AN 2006:161999

S. Oloff, S. Zhang, N. Sukumar, C.M. Breneman, and A. Tropsha, Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands based on Receptor Information (CoLiBRI), Journal of Chemical Information and Modeling, (2006), 46, 844-851.

Rege, Kaushal; Ladiwala, Asif; Hu, Shanghui; Breneman, Curt M.; Dordick, Jonathan S.; Cramer, Steven M. Investigation of DNA-Binding Properties of an Aminoglycoside-Polyamine Library Using Quantitative Structure-Activity Relationship (QSAR) Models. Journal of Chemical Information and Modeling ACS ASAP. CODEN: JCISD8 ISSN:1549-9596.

Ladiwala, Asif; Rege, Kaushal; Breneman, Curtis M.; Cramer, Steven M. A priori prediction of adsorption isotherm parameters and chromatographic behavior in ion-exchange systems. Proceedings of the National Academy of Sciences of the United States of America (2005), 102(33), 11710-11715.

Colon, Wilfredo; Chung, Jinhyuk; De Beus, Mitchell D.; Breneman, Curtis M.; Zhang, Hongmei. Compositions and methods for treating amyotrophic lateral sclerosis (als). PCT Int. Appl. (2005), 86 pp.

Lavine, Barry K.; Davidson, Charles E.; Breneman, Curt; Kaat, William. Genetic algorithms for classification of olfactory stimulants. Methods in Molecular Biology (Totowa, NJ, United States) (2004), 275(Chemoinformatics), 399-425.

Rege, Kaushal; Ladiwala, Asif; Tugcu, Nihal; Breneman, Curt M.; Cramer, Steven M. Parallel screening of selective and high-affinity displacers for proteins in ion-exchange systems. Journal of Chromatography, A (2004), 1033(1), 19-28.

Deng, Wei; Breneman, Curt; Embrechts, Mark J. Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods. Journal of Chemical Information and Computer Sciences (2004), 44(2), 699-703.

Song, Minghu; Breneman, Curt M.; Sukumar, N. Three-dimensional quantitative structure-activity relationship analyses of piperidine-based CCR5 receptor antagonists. Bioorganic & Medicinal Chemistry (2004), 12(2), 489-499.

Lavine, Barry K.; Davidson, Charles E.; Breneman, Curt; Katt, William. Electronic van der Waals Surface Property Descriptors and Genetic Algorithms for Developing Structure-Activity Correlations in Olfactory Databases. Journal of Chemical Information and Computer Sciences (2003), 43(6), 1890-1905.

Tugcu, Nihal; Ladiwala, Asif; Breneman, Curt M.; Cramer, Steven M. Identification of chemically selective displacers using parallel batch screening experiments and quantitative structure efficacy relationship models. Analytical Chemistry (2003), 75(21), 5806-5816.

Ladiwala, Asif; Rege, Kaushal; Breneman, Curt M.; Cramer, Steven M. Investigation of mobile phase salt type effects on protein retention and selectivity in cation-exchange systems using quantitative structure retention relationship models. Langmuir (2003), 19(20), 8443-8454.

Breneman, Curt M.; Sundling, C. Matthew; Sukumar, N.; Shen, Lingling; Katt, William P.; Embrechts, Mark J. New developments in PEST shape/property hybrid descriptors. Journal of Computer-Aided Molecular Design (2003), 17(2-4), 231-240.

Zagorevskii, Dmitri; Song, Minghu; Breneman, Curt; Yuan, Yang; Fuchs, Tarra; Gates, Kent S.; Greenlief, C. Michael. A mass spectrometry study of tirapazamine and its metabolites insights into the mechanism of metabolic transformations and the characterization of reaction intermediates. Journal of the American Society for Mass Spectrometry (2003), 14(8), 881-892.

Tugcu, Nihal; Song, Minghu; Breneman, Curt M.; Sukumar, N.; Bennett, Kristin P.; Cramer, Steven M. Prediction of the effect of mobile-phase salt type on protein retention and selectivity in anion exchange systems. Analytical Chemistry (2003), 75(14), 3563-3572.

Whitehead, C. E.; Breneman, C. M.; Sukumar, N.; Ryan, M. D. Transferable atom equivalent multicentered multipole expansion method. Journal of Computational Chemistry (2003), 24(4), 512-529.

Song, Minghu; Breneman, Curt M.; Bi, Jinbo; Sukumar, N.; Bennett, Kristin P.; Cramer, Steven; Tugcu, Nihal. Prediction of protein retention times in anion-exchange chromatography systems using support vector regression. Journal of Chemical Information and Computer Sciences (2002), 42(6), 1347-1357.

Mazza, Cecilia B.; Rege, Kaushal; Breneman, Curt M.; Sukumar, N.; Dordick, Jonathan S.; Cramer, Steven M. High-throughput screening and quantitative structure-efficacy relationship models of potential displacer molecules for ion-exchange systems. Biotechnology and Bioengineering (2002), 80(1), 60-72.

Mazza, C. B.; Whitehead, C. E.; Breneman, C. M.; Cramer, S. M. Predictive Quantitative Structure Retention Relationship models for ion-exchange chromatography. Chromatographia (2002), 56(3/4), 147-152.

Mazza, C. B.; Sukumar, N.; Breneman, C. M.; Cramer, S. M. Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure. Analytical Chemistry (2001), 73(22), 5457-5461.

Breneman, C. M.; Sundling, C. M.; Sukumar, N.; Shen, L.; Katt, W. P.; Embrechts, M. J. (2003) "New Developments in PEST Shape/Property Hybrid Descriptors" J. Comput.-Aided Mol.Design, 17, 231-240.

Breneman, C. M.; Bennett, K. P.; Embrechts, M. J.; Cramer, S. M.; Song, M.; Bi, J.; Sukumar, N. (2002) "Descriptor Generation, Selection and Model Building in Quantitative Structure-Property Analysis" in Experimental Design for Combinatorial and High Throughput Materials Development, Cawse, J. N. (ed), John Wiley, New York, 203-238.

Song, M.; Breneman, C. M.; Bi, J.; Sukumar, N.; Bennett, K. P.; Cramer S. M.; Tugcu, N. (2002) "Prediction of Protein Retention Times in Anion-exchange Chromatography Systems using Support Vector Regression" J. Chem. Inf. Comput. Sci., 42, 1347-1357.

Mazza, C. B. (2001) "Quantitative-Structure Based Predictions of Displacer and Protein Affinities in Chromatographic Systems" Ph.D. Thesis.

Mazza, C. B.; Sukumar, N.; Breneman, C. M.; Cramer, S. M. (2001) "Prediction of Protein Retention in Ion-Exchange Systems Using Molecular Descriptors Obtained from Crystal Structure" Analytical Chemistry, 73(22), 5457-5461.

Breneman, C. M.; Rhem M. (1997) "QSPR Analysis of HPLC Column Capacity Factors for a Set of High-Energy Materials Using Electronic Van Der Waals Surface Property Descriptors Computed by Transferable Atom Equivalent Method" J. Comp. Chem., 18(2), 182-197.

Rhem, M.O. (1996) RECON: An Algorithm for Molecular Charge Density Reconstruction Using Atomic Charge Density Fragments. Ph.D. Dissertation (Rensselaer Polytechnic Institute, Troy).

Breneman, C. M.; Thompson, T. R.; Rhem, M.; Dung, M. (1995) "Electron-Density Modeling of Large Systems Using the Transferable Atom Equivalent Method" Computers & Chemistry, 19(3), 161.

Presentations

Rensselaer Polytechnic Institute RECCR Home Page || Member Area || Wiki

Copyright ©2005 Rensselaer Polytechnic Institute
All rights reserved worldwide.