RECCR Rensselaer Exploratory Center for Cheminformatics Research

Presentation: Fuzzy Bar-code Representations of DNA-Protein Interactions

Predicting Target Sites of Transcription Factors

DNA Electronic Surface Property Reconstruction

DIXEL Coordinate System for DNA

Preliminary Studies of the Discriminant Potential of DIXELS

References

PI: Curt M. Breneman
Co-PI:N. Sukumar

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News Members Projects Publications Software Data MLI ECCRS
Beyond ATCG: “Dixel” representations of DNA-protein interactions

References

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.

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.; 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.

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.

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.

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. (2001a). "Prediction of Protein Retention in Ion-Exchange Systems Using Molecular Descriptors Obtained from Crystal Structure." Analytical Chemistry, 73(22), 5457-5461.

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. (2001a). "Prediction of Protein Retention in Ion-Exchange Systems Using Molecular Descriptors Obtained from Crystal Structure." Analytical Chemistry, 73(22), 5457-5461.

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.

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