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Curt M. Breneman Research Group

Publications

2004-00 || 2006-05 || 2009-07 || 2014-10

2014-2010

Thrimoorthy Potta; Zhuo Zhen; Taraka Sai Pavan Grandhi; Matthew D Christensen; James Ramos; Curt M Breneman & Kaushal Rege,"Discovery of antibiotics-derived polymers for gene delivery using combinatorial synthesis and cheminformatics modeling" (2014) in "Biomaterials", (35), Elsevier

Curt M Breneman; L Catherine Brinson; Linda S Schadler; Bharath Natarajan; Michael Krein; Ke Wu; Lisa Morkowchuk; Yang Li; Hua Deng & Hongyi Xu,"Stalking the Materials Genome: A Data-Driven Approach to the Virtual Design of Nanostructured Polymers" (2013) in "Advanced Functional Materials", (23), WILEY-VCH Verlag

Tao-wei Huang; Jed Zaretzki; Charles Bergeron; Kristin P Bennett & Curt M Breneman,"DR-Predictor: Incorporating flexible docking with specialized electronic reactivity and machine learning techniques to predict CYP-mediated sites of metabolism" (2013) in "Journal of chemical information and modeling", (53), American Chemical Society

Jed Zaretzki; Charles Bergeron; Tao-wei Huang; Patrik Rydberg; S Joshua Swamidass & Curt M Breneman,"RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules" (2013) in "Bioinformatics", (29), Oxford University Press

Michael Krein; Tao-Wei Huang; Lisa Morkowchuk; Dimitris K Agrafiotis & Curt M Breneman,"Developing Best Practices for Descriptor-Based Property Prediction: Appropriate Matching of Datasets, Descriptors, Methods, and Expectations" (2012) in "Statistical Modelling of Molecular Descriptors in QSAR/QSPR, Volume 2", Wiley-VCH Verlag GmbH & Co. KGaA

Michael P Krein; Bharath Natarajan; Linda S Schadler; LC Brinson; Hua Deng; Donghai Gai; Yang Li & Curt M Breneman,"Development of Materials Informatics Tools and Infrastructure to Enable High Throughput Materials Design" (2012) in , (1425)

Barry K Lavine; Collin White; Nikhil Mirjankar; C Matthew Sundling & Curt M Breneman,"Odor--Structure Relationship Studies of Tetralin and Indan Musks" (2012) in "Chemical senses", (37), Oxford University Press

N Sukumar; Sourav Das; Michael Krein; Rahul Godawat; Inna Vitol; Shekhar Garde; Kristin P Bennett & Curt M Breneman,"Molecular Descriptors for Biological Systems" (2012) in "Computational Approaches in Cheminformatics and Bioinformatics", John Wiley & Sons, Inc.

Charles Bergeron; Gregory Moore; Michael Krein; Curt M Breneman & Kristin P Bennett,"Exploiting domain knowledge for improved quantitative high-throughput screening curve fitting" (2011) in "Journal of chemical information and modeling", (51), American Chemical Society

Charles Bergeron; Michael Krein; Gregory Moore; Curt M Breneman & Kristin P Bennett,"Modeling Choices for Virtual Screening Hit Identification" (2011) in "Molecular Informatics", (30), WILEY-VCH Verlag

Margaret R McLellan; M Dominic Ryan & Curt M Breneman,"Rank Order Entropy: why one metric is not enough" (2011) in "Journal of chemical information and modeling", (51), American Chemical Society

Jed Zaretzki; Charles Bergeron; Patrik Rydberg; Tao-wei Huang; Kristin P Bennett & Curt M Breneman,"RS-Predictor: A new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4" (2011) in "Journal of chemical information and modeling", (51), American Chemical Society

Sourav Das; Michael P Krein & Curt M Breneman,"Binding affinity prediction with property-encoded shape distribution signatures" (2010) in "Journal of chemical information and modeling", (50), American Chemical Society

Sourav Das; Michael P Krein & Curt M Breneman,"PESDserv: a server for high-throughput comparison of protein binding site surfaces" (2010) in "Bioinformatics", (26), Oxford University Press

Patrik Rydberg; David E Gloriam; Jed Zaretzki; Curt Breneman & Lars Olsen,"SMARTCyp: A 2D method for prediction of cytochrome P450-mediated drug metabolism" (2010) in "ACS Medicinal Chemistry Letters", (1), American Chemical Society

2009-2007

Sourav Das; Arshad Kokardekar & Curt M Breneman,"Rapid comparison of protein binding site surfaces with property encoded shape distributions" (2009) in "Journal of chemical information and modeling", (49), American Chemical Society

Jared E Decker; J Chris Pires; Gavin C Conant; Stephanie D McKay; Michael P Heaton; Kefei Chen; Alan Cooper; Johanna Vilkki; Christopher M Seabury et al.,"Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics" (2009) in "Proceedings of the National Academy of Sciences", (106), National Acad Sciences

Christopher J Morrison; Curt M Breneman; JA Moore & Steven M Cramer,"Evaluation of chemically selective displacer analogues for protein purification" (2009) in "Analytical chemistry", (81), American Chemical Society

Charles Bergeron; Jed Zaretzki; Curt Breneman & Kristin P Bennett,"Multiple instance ranking" (2008) in

N Sukumar; Michael Krein & Curt M Breneman,"Bioinformatics and cheminformatics: Where do the twain meet?" (2008) in "Current opinion in drug discovery & development", (11)

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

Jie Chen; Ting Yang; Qiong Luo; Curt M Breneman & Steven M Cramer,"Investigation of protein retention in hydrophobic interaction chromatographic (HIC) systems using the preferential interaction theory and quantitative structure property relationship models" (2007) in "Reactive and Functional Polymers", (67), Elsevier

Sean Ekins; Mark J Embrechts; Curt M Breneman; Kam Jim & Jean-Pierre Wery,"Novel Applications of Kernel--Partial Least Squares to Modeling a Comprehensive Array of Properties for Drug Discovery" (2007) in "Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals", John Wiley & Sons, Inc.

Changjian Huang; Mark J Embrechts; Nagamani Sukumar & Curt M Breneman,"Data fusion and auto-fusion for quantitative structure-activity relationship (QSAR)" (2007) in "Artificial Neural Networks--ICANN 2007", Springer Berlin Heidelberg

Nagamani Sukumar & Curt M Breneman,"QTAIM in drug discovery and protein modeling" (2007) in "The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design", Wiley-VCH Verlag GmbH & Co. KGaA

Ting Yang; Curt M Breneman & Steven M Cramer,"Investigation of multi-modal high-salt binding ion-exchange chromatography using quantitative structure--property relationship modeling" (2007) in "Journal of Chromatography A", (1175), Elsevier

2006-2005

Asif Ladiwala; Fang Xia; Qiong Luo; Curt M Breneman & Steven M Cramer,"Investigation of protein retention and selectivity in HIC systems using quantitative structure retention relationship models" (2006) in "Biotechnology and bioengineering", (93), Wiley Subscription Services, Inc., A Wiley Company

Jia Liu; Ting Yang; Asif Ladiwala; Steven M Cramer & Curtis M Breneman,"High Throughput Determination and QSER Modeling of Displacer DC-50 Values for Ion Exchange Systems" (2006) in "Separation science and technology", (41), Taylor & Francis Group

Scott Oloff; Shuxing Zhang; Nagamani Sukumar; Curt Breneman & Alexander Tropsha,"Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI)" (2006) in "Journal of chemical information and modeling", (46), American Chemical Society

C. Matthew Sundling, Nagamani Sukumar, Hongmei Zhang, Mark J. Embrechts and Curt M. Breneman Wavelets in Chemistry and Cheminformatics, in Reviews in Computational Chemistry, in Press, 2005.

Scott Oloff, Shuxing Zhang, Nagamani Sukumar, Curt Breneman, and Alexander Tropsha Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands based on Receptor Information (CoLiBRI) (Journal of Chemical Information and Modeling, in press, 2005)

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.

2004-2000

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.

RECCR ©2005 Curt M. Breneman