A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 17-Sep-2014 number of released structures: 7399
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Publications

Papers from the NDB Project supported in total or in part by the NDB grants
(in reverse chronological order)

  1. S. Neidle, B. Schneider, H. M. Berman. (2009). Chapter 3 Fundamentals of DNA and RNA structure. In Structural Bioinformatics, Second Edition (P. E. Bourne & J. Gu, eds.). John Wiley & Sons, Inc., Hoboken, NJ.
  2. B. Schneider, J. D. L. Cruz, Z. Feng, L. Chen, S. Dutta, I. Persikova, J. D. Westbrook, H. Yang, J. Young, C. Zardecki, H. M. Berman. (2009). Chapter 12 The Nucleic Acid Database. In Structural Bioinformatics, Second Edition (J. Gu & P. E. Bourne, eds.), pp. 305-319. John Wiley & Sons, Inc., Hoboken, NJ.
  3. B. Schneider, H. M. Berman. (2006). Basics of Nucleic Acid Structure. Concepts, Tools, and Archives. In Computational approaches to nucleic acid structures. Concepts, Tools, and Archives. (J. Šponer & F. Lankaš, eds.), pp. 1-44. Springer, Berlin.
  4. W. Ge, B. Schneider, W. K. Olson. (2005) Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. Biophysical J 88: 1166-1190.
  5. W. A. McLaughlin, D. W. Kulp, J. de la Cruz, X.-J. Lu, C. Lawson, H. Berman. (2004) A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. Journal of Structural and Functional Genomics 5: 255-265.
  6. B. Schneider, Z. Moravek, H. M. Berman. (2004) RNA conformational classes. Nucleic Acids Res 32: 1666-1677.
  7. X. J. Lu, W. K. Olson. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31: 5108-5121.
  8. S. Neidle, B. Schneider, H. M. Berman. (2003). Fundamentals of DNA and RNA structure. In Structural Bioinformatics (P. E. Bourne & H. Weissig, eds.), pp. 41-73. John Wiley & Sons, Inc., Hoboken, NJ.
  9. Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., Westhof, E. (2003). Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Research 31.13: 3450-3460.
  10. Helen M. Berman and Wilma K. Olson (2003). "The Many Twists of DNA" DNA 50: The Secret of Life; Miriam Balaban, Editor Faircout, London: 104-124.
  11. Berman, H.M., Westbrook, J., Feng, Z., Iype, L., Schneider, B., Zardecki, C. (2003). The Nucleic Acid Database. Structural Bioinformatics. P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc.: 119-216.
  12. Berman, H.M., Westbrook, J., Feng, Z., Iype, L., Schneider, B., Zardecki, C. (2002): The Nucleic Acid Database. Acta Cryst. D58: 889-898
  13. Olson, WK, Bansal, M, Burley, SK, Dickerson, RE, Gerstein, M, Harvey, SC, Heinemann, U, Lu, X-J, Neidle, S, Shakked, Z, Sklenar, H, Suzuki, M, Tung, C-S, Westhof, E, Cynthia Wolberger, Berman, HM (2001): A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 313: 229-237.
  14. Berman, H.M., Feng, Z., Schneider, B., Westbrook, J., Zardecki, C. (2001). The Nucleic Acid Database (NDB). International Tables for Crystallography. M. G. Rossman and E. Arnold. Dordrecht, Kluwer Academic Publishers. F. Crystallography of Biological Macromolecules: 657-662.
  15. Clowney, L., Westbrook, J., and Berman, H.M., (1999) a la mode: a ligand and monomer object data environment. 1. Automated construction of mmCIF monomer and ligand models. J. Appl. Crystallogr. 32 125-133.
  16. Berman, H.M. and Schneider, B. (1999). Nucleic acid hydration, in Oxford Handbook of Nucleic Acid Structure. S. Neidle. Oxford, Oxford University Press: 295-312.
  17. Berman, H.M., Zardecki, C., and Westbrook, J., (1999) The Nucleic Acid Database: a research and teaching tool, in Oxford Handbook of Nucleic Acid Structure, S. Neidle, Editor. Oxford University Press, p. 77-92.
  18. Woda, J., Schneider, B., Patel, K., Mistry, K., and Berman, H.M. (1998). An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J. 75 2170-2177.
  19. Schneider, B., Patel, K., and Berman, H.M., (1998)Hydration of the phosphate group in double helical DNA. Biophys. J. 75 2422-2434.
  20. Westbrook, J.D., Hsieh, S.-H., and Fitzgerald, P.M.D. (1997). CIF applications. VI. CIFLIB: an application-program interface to CIF dictionaries and data files. J. Appl. Cryst. 30, 79-83.
  21. Schneider, B., Neidle, S., and Berman, H.M. (1997). Conformations of the sugar- phosphate backbone in helical DNA crystal structures. Biopolymers 42, 113-124.
  22. Berman, H.M., Clowney, L., Gelbin, A., Zardecki, C., and Westbrook, J.D., The network interface to the Nucleic Acid Database, in Proceedings of the Macromolecular Crystallography Computing School at Western Washington University, P. Bourne and K. Watenpaugh, Editor. (1997). San Diego Supercomputing Center: 271-285
  23. Berman, H.M. (1997). Crystal studies of B-DNA: the answers and the questions. Biopolymers 44, 23-44.
  24. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A.T., and Berman, H.M. (1996). New parameters for the refinement of nucleic acid containing structures. Acta Crystallogr. D52, 57-64.
  25. Olson, W.K. and Zhurkin, V.B., Twenty years of DNA bending, in Biological structure and dynamics. 2. Proceedings of the ninth conversation in the discipline biomolecular stereodynamics held at the State University of New York at Albany, R.H. Sarma and M.H. Sarma, Editor. (1996). Adenine Press: NY. 341- 370.
  26. Olson, W.K. (1996). Simulating DNA at low resolution. Curr. Opin. Cell. Biol. 6, 242-256.
  27. Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W.K., and Berman, H.M. (1996). Geometric parameters in nucleic acids: sugar and phosphate constituents. J. Am. Chem. Soc. 118(3), 519-528.
  28. Gelbin, A., Clowney, L., Hsieh, S.-H., Zardecki, C., Westbrook, J., and Berman, H.M. (1996). Surveying and classifying nucleic acid structures. Acta Crystallogr. A52 Supplement, PS04.04.12.
  29. Clowney, L., Jain, S.C., Srinivasan, A.R., Westbrook, J., Olson, W.K., and Berman, H.M. (1996). Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc. 118, 509-518.
  30. Berman, H.M., Gelbin, A., and Westbrook, J. (1996). Nucleic acid crystallography: a view from the nucleic acid database. Prog. Biophys. Mol. Biol. 66, 255-288.
  31. Berman, H.M., Gelbin, A., Clowney, L., Hsieh, S.-H., Zardecki, C., and Westbrook, J. (1996). The Nucleic Acid Database: present and future. J. Res. Natl. Inst. Stand. Technol. 101(3), 243-257.
  32. Berman, H.M., Beveridge, D.L., Neidle, S., Olson, W.K., Westbrook, J., Gelbin, A., Hsieh, S.-H., Clowney, L., Schneider, B., and Zardecki, C., The Nucleic Acid Database project, in Biological structure and dynamics. 2. Proceedings of the ninth conversation in the discipline biomolecular stereodynamics held at the State University of New York at Albany, R.H. Sarma and M.H. Sarma, Editor. (1996). Adenine Press: NY. 1-13.
  33. Young, M.A., Ravishanker, G., Beveridge, D.L., and Berman, H.M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA- protein complexes. Biophys. J. 68, 2454-2468.
  34. Schneider, B. and Berman, H.M. (1995). Hydration of the DNA bases is local. Biophys. J. 69, 2661-2669.
  35. Olson, W.K., Babcock, M.S., Gorin, A., Liu, G., Marky, N.L., Martino, J.A., Pedersen, S.C., Srinivasan, A.R., Tobias, I., Westcott, T.P., and Zhang, P. (1995). Flexing and folding double helical DNA. Biophys. Chem. 55, 7-29.
  36. Gorin, A.A., Zhurkin, V.B., and Olson, W.K. (1995). B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247(1), 34-48.
  37. Cohen, D.M., Kulikowski, C., and Berman, H. (1995). DEXTER: a system that experiments with choices of training data using expert knowledge in the domain of DNA hydration. Machine Learning 21, 81-101.
  38. Young, M.A., Nirmala, R., Srinivasan, J., McConnell, K.J., Ravishanker, G., Beveridge, D.L., and Berman, H.M., Analysis of helix bending in crystal structures and molecular dynamics simulations of DNA oligonucleotides, in Structural biology: the state of the art. 2. Proceedings of the eight conversation in the discipline biomolecular stereodynamics held at the State University of New York at Albany, R.H. Sarma and M.H. Sarma, Editor. (1994). Adenine Press: NY. 197-214.
  39. Srinivasan, A.R. and Olson, W.K. (1994). Computer models of DNA four-way junctions. Biochemistry 33, 9389-9404.
  40. Schneider, B., Cohen, D.M., Schleifer, L., Srinivasan, A.R., Olson, W.K., and Berman, H.M. (1993). A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J. 65, 2291-2303.
  41. Cohen, D.M., Kulikowski, C., and Berman, H.M., Knowledge-based generation of machine learning experiments: learning DNA crystallography data, in Proceedings of the first intelligent systems in molecular biology, D.S. L. Hunter J. Shavlik, Editor. (1993). AAAI/MIT Press: 92-100.
  42. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A.R., and Schneider, B. (1992). The Nucleic Acid Database - a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63(3), 751-759.