Keywords
Last Name
Institution

Curtis Breneman

TitleProfessor
InstitutionRensselaer Polytechnic Institute
DepartmentChemistry
Address

     Bibliographic 
     selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Potta T, Zhen Z, Grandhi TS, Christensen MD, Ramos J, Breneman CM, Rege K. Discovery of antibiotics-derived polymers for gene delivery using combinatorial synthesis and cheminformatics modeling. Biomaterials. 2014 Feb; 35(6):1977-88.
      View in: PubMed
    2. Huang TW, Zaretzki J, Bergeron C, Bennett KP, Breneman CM. DR-Predictor: Incorporating Flexible Docking with Specialized Electronic Reactivity and Machine Learning Techniques to Predict CYP-Mediated Sites of Metabolism. J Chem Inf Model. 2013 Dec 23; 53(12):3352-66.
      View in: PubMed
    3. Shoulder JM, Alderman NS, Breneman CM, Nyman MC. Polycyclic aromatic hydrocarbon reaction rates with peroxy-acid treatment: prediction of reactivity using local ionization potential. SAR QSAR Environ Res. 2013 Aug; 24(8):611-24.
      View in: PubMed
    4. Pilania G, Wang CC, Wu K, Sukumar N, Breneman C, Sotzing G, Ramprasad R. New Group IV chemical motifs for improved dielectric permittivity of polyethylene. J Chem Inf Model. 2013 Apr 22; 53(4):879-86.
      View in: PubMed
    5. Zaretzki J, Bergeron C, Huang TW, Rydberg P, Swamidass SJ, Breneman CM. RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules. Bioinformatics. 2013 Feb 15; 29(4):497-8.
      View in: PubMed
    6. Lavine BK, White C, Mirjankar N, Sundling CM, Breneman CM. Odor-structure relationship studies of tetralin and indan musks. Chem Senses. 2012 Oct; 37(8):723-36.
      View in: PubMed
    7. Bergeron C, Moore G, Zaretzki J, Breneman CM, Bennett KP. Fast bundle algorithm for multiple-instance learning. IEEE Trans Pattern Anal Mach Intell. 2012 Jun; 34(6):1068-79.
      View in: PubMed
    8. Zaretzki J, Rydberg P, Bergeron C, Bennett KP, Olsen L, Breneman CM. RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes. J Chem Inf Model. 2012 Jun 25; 52(6):1637-59.
      View in: PubMed
    9. Bergeron C, Moore G, Krein M, Breneman CM, Bennett KP. Exploiting domain knowledge for improved quantitative high-throughput screening curve fitting. J Chem Inf Model. 2011 Nov 28; 51(11):2808-20.
      View in: PubMed
    10. McLellan MR, Ryan MD, Breneman CM. Rank order entropy: why one metric is not enough. J Chem Inf Model. 2011 Sep 26; 51(9):2302-19.
      View in: PubMed
    11. Zaretzki J, Bergeron C, Rydberg P, Huang TW, Bennett KP, Breneman CM. RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4. J Chem Inf Model. 2011 Jul 25; 51(7):1667-89.
      View in: PubMed
    12. Das S, Krein MP, Breneman CM. PESDserv: a server for high-throughput comparison of protein binding site surfaces. Bioinformatics. 2010 Aug 1; 26(15):1913-4.
      View in: PubMed
    13. Das S, Krein MP, Breneman CM. Binding affinity prediction with property-encoded shape distribution signatures. J Chem Inf Model. 2010 Feb 22; 50(2):298-308.
      View in: PubMed
    14. Das S, Kokardekar A, Breneman CM. Rapid comparison of protein binding site surfaces with property encoded shape distributions. J Chem Inf Model. 2009 Dec; 49(12):2863-72.
      View in: PubMed
    15. Morrison CJ, Breneman CM, Moore JA, Cramer SM. Evaluation of chemically selective displacer analogues for protein purification. Anal Chem. 2009 Aug 1; 81(15):6186-94.
      View in: PubMed
    16. Sukumar N, Krein M, Breneman CM. Bioinformatics and cheminformatics: where do the twain meet? Curr Opin Drug Discov Devel. 2008 May; 11(3):311-9.
      View in: PubMed
    17. Yang T, Sundling MC, Freed AS, Breneman CM, Cramer SM. Prediction of pH-dependent chromatographic behavior in ion-exchange systems. Anal Chem. 2007 Dec 1; 79(23):8927-39.
      View in: PubMed
    18. Yang T, Breneman CM, Cramer SM. Investigation of multi-modal high-salt binding ion-exchange chromatography using quantitative structure-property relationship modeling. J Chromatogr A. 2007 Dec 14; 1175(1):96-105.
      View in: PubMed
    19. Chen J, Luo Q, Breneman CM, Cramer SM. Classification of protein adsorption and recovery at low salt conditions in hydrophobic interaction chromatographic systems. J Chromatogr A. 2007 Jan 19; 1139(2):236-46.
      View in: PubMed
    20. Ladiwala A, Xia F, Luo Q, Breneman CM, Cramer SM. Investigation of protein retention and selectivity in HIC systems using quantitative structure retention relationship models. Biotechnol Bioeng. 2006 Apr 5; 93(5):836-50.
      View in: PubMed
    21. Oloff S, Zhang S, Sukumar N, Breneman C, Tropsha A. Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI). J Chem Inf Model. 2006 Mar-Apr; 46(2):844-51.
      View in: PubMed
    22. Rege K, Ladiwala A, Hu S, Breneman CM, Dordick JS, Cramer SM. Investigation of DNA-binding properties of an aminoglycoside-polyamine library using quantitative structure-activity relationship (QSAR) models. J Chem Inf Model. 2005 Nov-Dec; 45(6):1854-63.
      View in: PubMed
    23. Ladiwala A, Rege K, Breneman CM, Cramer SM. A priori prediction of adsorption isotherm parameters and chromatographic behavior in ion-exchange systems. Proc Natl Acad Sci U S A. 2005 Aug 16; 102(33):11710-5.
      View in: PubMed
    24. Rege K, Ladiwala A, Tugcu N, Breneman CM, Cramer SM. Parallel screening of selective and high-affinity displacers for proteins in ion-exchange systems. J Chromatogr A. 2004 Apr 9; 1033(1):19-28.
      View in: PubMed
    25. Deng W, Breneman C, Embrechts MJ. Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods. J Chem Inf Comput Sci. 2004 Mar-Apr; 44(2):699-703.
      View in: PubMed
    26. Song M, Breneman CM, Sukumar N. Three-dimensional quantitative structure-activity relationship analyses of piperidine-based CCR5 receptor antagonists. Bioorg Med Chem. 2004 Jan 15; 12(2):489-99.
      View in: PubMed
    27. Lavine BK, Davidson CE, Breneman C, Kaat W. Genetic algorithms for classification of olfactory stimulants. Methods Mol Biol. 2004; 275:399-426.
      View in: PubMed
    28. Lavine BK, Davidson CE, Breneman C, Katt W, Sundling CM. Electronic van der Waals surface property descriptors and genetic algorithms for developing structure-activity correlations in olfactory databases. J Chem Inf Comput Sci. 2003 Nov-Dec; 43(6):1890-905.
      View in: PubMed
    29. Tugcu N, Ladiwala A, Breneman CM, Cramer SM. Identification of chemically selective displacers using parallel batch screening experiments and quantitative structure efficacy relationship models. Anal Chem. 2003 Nov 1; 75(21):5806-16.
      View in: PubMed
    30. Zagorevskii D, Song M, Breneman C, Yuan Y, Fuchs T, Gates KS, Greenlief CM. A mass spectrometry study of tirapazamine and its metabolites. insights into the mechanism of metabolic transformations and the characterization of reaction intermediates. J Am Soc Mass Spectrom. 2003 Aug; 14(8):881-92.
      View in: PubMed
    31. Tugcu N, Song M, Breneman CM, Sukumar N, Bennett KP, Cramer SM. Prediction of the effect of mobile-phase salt type on protein retention and selectivity in anion exchange systems. Anal Chem. 2003 Jul 15; 75(14):3563-72.
      View in: PubMed
    32. Whitehead CE, Breneman CM, Sukumar N, Ryan MD. Transferable atom equivalent multicentered multipole expansion method. J Comput Chem. 2003 Mar; 24(4):512-29.
      View in: PubMed
    33. Breneman CM, Sundling CM, Sukumar N, Shen L, Katt WP, Embrechts MJ. New developments in PEST shape/property hybrid descriptors. J Comput Aided Mol Des. 2003 Feb-Apr; 17(2-4):231-40.
      View in: PubMed
    34. Song M, Breneman CM, Bi J, Sukumar N, Bennett KP, Cramer S, Tugcu N. Prediction of protein retention times in anion-exchange chromatography systems using support vector regression. J Chem Inf Comput Sci. 2002 Nov-Dec; 42(6):1347-57.
      View in: PubMed
    35. Mazza CB, Rege K, Breneman CM, Sukumar N, Dordick JS, Cramer SM. High-throughput screening and quantitative structure-efficacy relationship models of potential displacer molecules for ion-exchange systems. Biotechnol Bioeng. 2002 Oct 5; 80(1):60-72.
      View in: PubMed
    36. Mazza CB, Sukumar N, Breneman CM, Cramer SM. Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure. Anal Chem. 2001 Nov 15; 73(22):5457-61.
      View in: PubMed
    37. Kewley RH, Embrechts MJ, Breneman C. Data strip mining for the virtual design of pharmaceuticals with neural networks. IEEE Trans Neural Netw. 2000; 11(3):668-79.
      View in: PubMed
    38. Wiberg KB, Hadad CM, Breneman CM, Laidig KE, Murcko MA, Lepage TJ. The response of electrons to structural changes. Science. 1991 May 31; 252(5010):1266-72.
      View in: PubMed
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