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

Publications

Curt M. Breneman

Kristin P. Bennett

Chris Bystroff

Wilfredo Colón

Steven Cramer

Mark J. Embrechts

Angel Garcia

Shekhar Garde

James A. Moore

Mark P. Wentland

Mohammed Zaki

News Members Projects Publications Software Data MLI ECCRS
Publications

Curt M. Breneman

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.

Changjian Huang, Mark J. Embrechts, Nagamani Sukumar, Curt M. Breneman, "Data Fusion and Auto-fusion for Quantitative Structure-Activity Relationship (QSAR)?" Artificial Neural Networks - ICANN(1) 2007, Lecture Notes in Computer Science, 628-637 (Springer 2007).

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.

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Kristin P. Bennett

Z. Xiang and K. P. Bennett, Multitask Transfer Using Multiple Latent Analysis, workshop on Inductive Transfer: 10 Years Later Workshop at Neural Information Processing Systems Conference, December 2005, Whistler, Canada.

K. Bennett, C. Bergeron, E. Acar, R. Klees. S. Vandenberg, B. Yener, and G. Plopper, Multiple routes to the osteogenic phenotype in mesenchymal stem cells, BMC Genomics, under review, 2007.

G. Kunapuli, K. Bennett, J. Hu, and J.-S. Pang, Classification Model Selection via Bilevel Programming, Computational Optimization and Applications, to appear 2007.

P. Agius, B. Kreiswirth, N. Kurepina, and K. P. Bennett, Typing Staphylococcus aureus using the spa gene and novel distance measures, IEEE Transactions on Computational Biology and Bioinformatics, to appear, 2007.

R. Klees, R. Salasznyk, S. Vandenberg, K. Bennett, and G. Plopper, "Laminin-5 Activates Extracellular Matrix Production and Osteogenic Gene Focusing in Human Mesenchymal Stem Cells", Matrix Biology, 2007.

L. Han, M. Embrechts and K. Bennett, Kernel-based Multiple Response Latent Analysis with Entropy Loss Function, submitted to International Joint Conference on Neural Networks, 2007.

Kristin P. Bennett, Emilio Parrado-Hernandez, The Interplay of Optimization and Machine Learning Research, Journal of Machine Learning Research,7(Jul):1265--1281, 2006.

I. Vitol, J. Driscoll, B. Kreiswirth, N. Kurepina, and K. P. Bennett, Identifying Mycobacterium tuberculosis complex Families using Spoligotypes, Infection, Genetics and Evolution, Nov;6(6):491- 504, 2006.

K. P. Bennett, J. Hu, G. Kunapuli, and J.-S. Pang, "Model Selection via Bilevel Optimization", Proceedings of the International Joint Conference in Neural Networks, Vancouver, 2006.

Zhiwei Zhu, Qiang Ji, Kristin P. Bennett: Nonlinear Eye Gaze Mapping Function Estimation via Support Vector Regression. ICPR (1) 2006: 1132-1135

Momma, M.; Bennett, K. (2005) "Constructing Orthogonal Latent Features for Arbitrary Loss", Feature Extraction, Foundations and Applications, Isabelle Guyon, Steve Gunn, Masoud Nikravesh, and Lofti Zadeh, editors, Springer, 2006.

Xiang, Z ; Bennett, K. , Cramer, S ; Breneman, C. Inductive Transfer using Kernel Multitask Latent Analysis, Proceedings or Workshop on Inductive Transfer, Neural Information Processing Systems, December 2005.

Bennett K. P.; Embrechts M. J. (2003) "An Optimization Perspective on Kernel Partial Least Squares Regression" in J.A.K. Suykens et. al., eds., Advances in Learning Theory: Methods, Models and Applications, NATO-ASI Series in Computer and System Sciences, IOS Press, Amsterdam, The Netherlands, 227-246.

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.

Campbell, C.; Bennett, K. P. (2001) "A Linear Programming Approach to Novelty Detection" Advances in Neural Information Processing Systems, Vol. 14, MIT Press.

Bennett, K.; Campbell, C. (2000) SIGKDD Explorations 2, 1-13.

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Christopher Bystroff

Zujun Shentu, Mohammad Hasan, Chris Bystroff, Mohammed J. Zaki Context Shapes: Efficient Complementary Shape Matching for Protein- Protein Docking, accepted for publication in Proteins: Structure, Function and Bioinformatics (forthcoming; in production).

Bystroff C. & Krogh A. (2006) Hidden Markov Models for Prediction of Protein Features, in Protein Structure Prediction: Methods and Protocols 2 nd Ed (Zaki, Bystroff, eds.) (to appear)

Huang Y-M & Bystroff C. (2006). Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions. Bioinformatics 22(4):413-420

Yuan X & Bystroff C. (2005). Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins. Bioinformatics 21(7):1010-1019

Bystroff C, Shao Y & Yuan X. (2004). Five heirarchical levels of sequence-structure correlation in proteins. Applied Bioinformatics 3(2):97-104

Zaki MJ, Nadimpally V, Bardhan D, & Bystroff C. (2004). Predicting Protein Folding Pathways. Bioinformatics 20 Suppl. 1, i387-i393. abstract PDF

Hou Y, Hsu W, Lee ML & Bystroff C. (2004). Remote Homology Detection Using Local Sequence-structure Correlations. Proteins 57(3):518-30.

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Wilfredo Colón

Manning, M.; Colón, W. (2004) "Structural Basis of Protein Kinetic Stability: Resistance to Sodium Dodecyl Sulfate Suggests a Central Role for Rigidity and a Bias towards Beta Sheet Structure." Biochemistry, 43, 11248-11254.

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Steven Cramer

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

Jia Liu, Ting Yang, Asif Ladiwala, and Steven M. Cramer, "High Throughput Determination and QSER Modeling of Displacer DC-50 Values for Ion Exchange Systems" Separation Science and Technology, 41: 30793107, 2006
ISSN 0149-6395 print 1520-5754 online DOI: 10.1080/01496390600894822

Jia Liu, Sun K. Park, J. A. Moore and Steven M. Cramer, "The Effect of Displacer Chemistry on Displacer Efficacy for a Sugar-based Anion Exchange Displacer Library, Industrial Engeineering & Chemistry Research, 45(26), 9107-9114.

Tugcu, N.; Park, S. K.; Moore, J. A.; Cramer, S. M. (2002) "Synthesis and Characterization of High-Affinity, Low-Molecular-Mass Displacers for Anion-Exchange Chromatography" Industrial and Engineering Chemistry Research, 41, 6482.

Mazza, C. B.; Rege, K; Breneman, C. M.; Sukumar, N.; Dordick, J. S.; Cramer, S. M. (2002) "High-Throughput Screening and Quantitative Structure-Efficacy Relationship Models of Potential Displacer Molecules for Ion-Exchange Systems" Biotechnology and Bioengineering, 80(1), 60-72.

Mazza, C. B.; Whitehead, C. E.; Breneman, C. M.; Cramer, S. M. (2002) "Predictive Quantitative Structure Retention Relationship Models for Ion-Exchange Chromatography" Chromatographia, 56(3-4), 147-152.

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.

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Mark J. Embrechts

Embrechts, Mark J.; Ekins, Sean. Classification of metabolites with kernel-partial least squares (K-PLS). Drug Metabolism and Disposition (2007), 35(3), 325-327.

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

Embrechts, M. J.; Szymanski, B.; Sternickel, M. (2004) "Introduction to Scientific Data Mining: Direct Kernel Methods and Applications" Chapter 10 in Computationally Intelligent Hybrid Systems, Ovaska, S. J., Ed., Wiley Interscience, 317-363.

Embrechts, M. J.; Bress, R. C.; Kewley, R. H. (2004) "Feature Selection via Senitivity Analysis with Direct Kernel PLS" to be published in Guyon, I., and Gunn, S., Eds., Feature Selection in Machine Learning, Springer Verlag.

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

Embrechts, M. J.; Arciniegas, F. A.; Ozdemir, M.; Kewley, R. H. (2003) "Data Mining for Molecules with 2-D Neural Network Sensitivity Analysis" International Journal of Smart Engineering System Design, 5, 225-239.

Bennett K. P.; Embrechts M. J. (2003) "An Optimization Perspective on Kernel Partial Least Squares Regression"in J.A.K. Suykens et. al., eds., Advances in Learning Theory: Methods, Models and Applications, NATO-ASI Series in Computer and System Sciences, IOS Press, Amsterdam, The Netherlands, 227-246.

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.

Kewley, R. H.; Embrechts, M. J.; Breneman, C. M. (2000) "Data Strip Mining for the Virtual Design of Pharmaceuticals with Neural Networks" IEEE Transactions on Neural Networks, 11(3), 668-679.

Embrechts, M. J., Breneman, C.M., (1999 ) "Supervised GA-based Regression Clustering for Data Mining Molecular Properties" Proceedings 216th American Chemical Society National Meeting, Anaheim, CA.

Kewley, Jr.,R., Embrechts, M. J., Breneman, C.M.,( 1998) "Neural Network Analysis for Data Strip Mining Problems" in Intelligent Engineering Systems through Artificial Neural Networks, v 8, C. Dagli et al., eds., 391 - 396, ASME Press,.

Embrechts, M. J., Kewley, Jr., R., Breneman, C.M. (1998) "Computationally Intelligent Data Mining for the Automated Discovery of Novel Pharmaceuticals" in Intelligent Engineering Systems through Artificial Neural Networks; v 8, C. Dagli et al., eds., 397 - 403, ASME Press.

Embrechts, M. J., Breneman, C.M.( 1998) "Data mining with neural networks for the prediction and understanding of molecular properties" Proceedings 215th American Chemical Society National Meeting, Dallas, TX.

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Angel Garcia

Petrone, P. M. and A. E. Garcia (2004) "MHC-peptide binding is assisted by bound water molecules" Journal of Molecular Biology 338(2): 419-435.

Garcia, A. E. and G. Hummer (2000) "Water penetration and escape in proteins." Proteins 38(3): 261-72.

Garcia, A. E., G. Hummer, et al. (1997) "Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation." Proteins 27(4): 471-80.

Garde, S., G. Hummer, et al. (1996) "Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes" Physical Review. E. Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 53(5): R4310-R4313.

Hummer, G., A. E. Garcia, et al. (1996) "A statistical mechanical description of biomolecular hydration" Faraday Discuss(103): 175-89.

Hummer, G., A. E. Garcia, et al. (1995) "Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes" Biophys J 68(5): 1639-52.

Hummer, G., A. E. Garcia, et al. (1995) "Hydration of Nucleic-Acid Fragments : Comparison of Theory and Experiment for High-Resolution Crystal-Structures of Rna ; DNA ; and DNA-Drug Complexes" Biophysical Journal 68(5): 1639-1652.

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Shekhar Garde

Yang, Lu; Garde, Shekhar. Modeling the selective partitioning of cations into negatively charged nanopores in water. Los Alamos National Laboratory, Preprint Archive, Physics (2007), 1-22, arXiv:physics/0702065.

Athawale, Manoj V.; Goel, Gaurav; Ghosh, Tuhin; Truskett, Thomas M.; Garde, Shekhar. Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Los Alamos National Laboratory, Preprint Archive, Condensed Matter (2007), 1-24, arXiv:cond-mat/0701676.

Tikhonov, Aleksey M.; Patel, Harshit; Garde, Shekhar; Schlossman, Mark L. Tail Ordering Due to Headgroup Hydrogen Bonding Interactions in Surfactant Monolayers at the Water-Oil Interface. Journal of Physical Chemistry B (2006), 110(39), 19093-19096.

Jain, Sandeep; Garde, Shekhar; Kumar, Sanat K. Do Inverse Monte Carlo Algorithms Yield Thermodynamically Consistent Interaction Potentials? Industrial & Engineering Chemistry Research (2006), 45(16), 5614-5618.

Pereira, Brian; Jain, Sandeep; Garde, Shekhar. Quantifying the protein core flexibility through analysis of cavity formation. Journal of Chemical Physics (2006), 124(7), 074704/1-074704/5.

Pereira Brian; Jain Sandeep; Garde, Shekhar Quantifying the protein core flexibility through analysis of cavity formation. The Journal of chemical physics (2006), 124(7), 74704.

B. Pereira, S. Jain, S. Sarupria, L. Yang, and S. Garde, "Pressure dependence of compressibility of a micelle and a protein: Insights from cavity formation analysis", Molecular Physics, accepted, (2006).

Pereira Brian; Jain Sandeep; Garde Shekhar Quantifying the protein core flexibility through analysis of cavity formation. The Journal of chemical physics (2006), 124(7), 74704. Journal code: 0375360. ISSN:0021-9606. PubMed ID 16497067 AN 2006111166 In-process for MEDLINE (Copyright (C) 2006 U.S. National Library of Medicine on SciFinder (R))

M. V. Athawale, G. Goel, T. Ghosh, T. M. Truskett, and S. Garde, "Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water", in review, Proc. Natl. Acad. Sci., 2006.

Pereira, Brian; Jain, Sandeep; Garde, Shekhar. Quantifying the protein
core flexibility through analysis of cavity formation. Journal of Chemical Physics (2006), 124(7), 074704/1-074704/5. CODEN: JCPSA6 ISSN:0021-9606. CAN 144:288147 AN 2006:182792

S. Jain, S. Garde, and S. Kumar, Do inverse Monte Carlo algorithms yield thermodynamically consistent interaction potentials?, in press, Ind. Eng. Chem. Res., (2006).

Garde, S., G. Hummer, et al. (1996) "Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes" Physical Review. E. Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 53(5): R4310-R4313.

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James A. Moore

Jia Liu, Sun K. Park, J. A. Moore and Steven M. Cramer, "The Effect of Displacer Chemistry on Displacer Efficacy for a Sugar-based Anion Exchange Displacer Library, Industrial Engeineering & Chemistry Research, 45(26), 9107-9114.

Rege, K.; Hu, S.; Moore, J. A.; Dordick J. S.; Cramer S. M. (2004) "Chemoenzymatic Synthesis and High-Throughput Screening of an Aminoglycoside-Polyamine Library: Identification of High-Affinity Displacers and DNA-Binding Ligands" Journal of the American Chemical Society, 126(39), 12306-12315.

Tugcu, N.; Bae, S. S.; Moore J. A.; Cramer, S. M. (2002) "Stationary Phase Effects on the Dynamic Affinity of Low Molecular Mass Displacers" Journal of Chromatography, A, 954 (1-2), 127-135.

Tugcu, N.; Park, S. K.; Moore, J. A.; Cramer, S. M. (2002) "Synthesis and Characterization of High-Affinity, Low-Molecular-Mass Displacers for Anion-Exchange Chromatography" Industrial and Engineering Chemistry Research, 41, 6482.

Tugcu, N.; Deshmukh, R. J.; Sanghvi, Y. S.; Moore, J. A.; Cramer S. M. (2001) "Purification of Oligonucleotides at High Column Loading by High Affinity, Low Molecular Weight Displacers" J. Chromatog., 923 (1-2), 65.

Shukla, A. A.; Deshmukh, R. R.; Moore, J. A.; Cramer, S. M. (2000) "Purification of Oligonucleotides by High Affinity, Low Molecular Weight Displacers." Biotechnology Progress, 16(6), 1064-1070.

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Mark P. Wentland

Wentland, Mark P. Preparation of 4-hydroxybenzomorphan derivatives for use in pharmaceutical compositions as opioid receptor ligands. PCT Int. Appl. (2006), 46 pp. CODEN: PIXXD2 WO 2006052710 A1 20060518 CAN 144:468351 AN 2006:469817

Bidlack, J. M.; (2002) Cohen, D. J.; McLaughlin, J. P.; Lou, R.; Ye, Y.; Wentland, M. P. "8-Carboxamidocyclazocine: A Long-Acting, Novel Benzomorphan" J. Pharmacol. Exp. Ther., 302, 374-380.

Wentland, M. P.; Lou, R.; Ye, Y.; Cohen, D. J.; Richardson, G. P.; Bidlack, J. M. (2001) "8-Carboxamidocyclazocine Analogues: Redefining the Structure-Activity Relationships of 2,6-Methano-3-benzazocines" Bioorg. Med. Chem. Lett., 11, 623-626.

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Mohammed Zaki

Zujun Shentu, Mohammad Hasan, Chris Bystroff, Mohammed J. Zaki Context Shapes: Efficient Complementary Shape Matching for Protein- Protein Docking, accepted for publication in Proteins: Structure, Function and Bioinformatics (forthcoming; in production).

Zaki, Mohammed J.; Sequeira, Karlton. Data mining in computational biology. Handbook of Computational Molecular Biology (2006), 38/1-38/26.

Zhang Yongqiang; Zaki, Mohammed J EXMOTIF: efficient structured motif extraction. Algorithms for molecular biology : AMB (2006), 1 21.

Zhang Yongqiang; Zaki, Mohammed J SMOTIF: efficient structured pattern and profile motif search. Algorithms for molecular biology : AMB (2006), 1 22.

Zaki, M.J. (2005) "Efficiently Mining Frequent Embedded Unordered Trees." Fundamenta Informaticae, 65, 1-20.

Zaki M.J.; Parimi, N.; De, N.; Gao, F.; Phoophakdee, B.; Urban, J.; Chaoji, V.; Al Hasan, M.; Salem, S. (2005) "Towards Generic Pattern Mining" Proceedings of the International Conference on Formal Concept Anaysis, 1-20

Zaki, M.J. (2001) "SPADE: An Efficient Algorithm for Mining Frequent Sequences" Machine Learning Journal, special issue on Unsupervised Learning (Doug Fisher, ed.), 42(1/2), 31-60.

Zaki, M.J. (2000) "Scalable Algorithms for Association Mining" EEE Transactions on Knowledge and Data Engineering, 12(3), 372-390.

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Michael Zuker

Markham, N. R. & Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res., 33, W577-W581.

M. Zuker Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-15, (2003)

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