Senior Investigator: Jacob V. Maizel, Jr.

    Affiliation: Chief, Laboratory of Experimental and Computational Biology, CCR, NCI.

    Research: Analysis of biosequences by computational methods for detection of relationships between genes or proteins, discovery of sequence patterns, and prediction of secondary and tertiary structure.

    Prediction of RNA 2D and 3D structure in HIV, retroviruses, picornaviruses, and other RNA using methods developed here to find unusual folding regions and correlate their structure with biological functions.

   Employ massively parallel and vector supercomputers with high-performance code to study challenging problems in computational biology with the long-range goal of predicting atomic structures from gene sequences.

   Personnel

        RNA structure prediction and analysis
           S. Le (RNA secondary structure of HIV and other RNA)
           J. Chen (ABCC, optimization of codes for massively parallel and vector supercomputers.
           H. Martinez (automatic construction of 3D RNA models from 2D predictions)

   For early papers covering work on the development of SDS gel electrophoresis, discoveries on poliovirus and adenovirus structure and replication, electron microscopy of genome mapping and nucleic acid structure and early sequence analysis see my complete bibliography.

   Recent publications:

 155.Chen, Jih-H., Le, S-Y., Shapiro, B. A., and Maizel, J. V.: Optimization of an RNA folding algorithm for parallel architectures. Parallel Computing 24: 1617-1634, 1998.

 156.Le, S-Y., Liu, W-M., and Maizel, J. V., Jr.: Phylogenetic evidence for the improved RNA higher-order structure in internal ribosome entry sequences of HCV and pestiviruses. Virus Genes 17(3): 279-295, 1998.

157.Le, S-Y., Chen, J-H., Pattabiraman, N., and Maizel, J. V., Jr.: Ion-RNA interactions in the RNA pseudoknot of a ribosomal frameshifting site: Molecular modeling studies. J. Biomol. Struct. Dyn. 16(1): 1-11, 1998.

158.Le, S. Y. and Maizel, J. V., Jr.: Evolution of a common structural core in the internal ribosome entry sites of picornavirus.Virus Genes 16(1): 25-38, 1998.

 159.Pramodh, V., Pattabiraman, N., Le, S-Y., and Maizel, J. V., Jr.: A molecular modeling study of antibiotics-RNA interactions: Application to HIV-1 Rev response element. J. Mol. Struct. (Theo. Chem.) 423: 125-136, 1998.

 160.Vishveshwara, S., Jacob, R., Nadig, G., and Maizel, Jr., J. V.: The role of lysine-41 in RNase A catalysis A quantum chemical study on the active site-ligand complex. J. Mol. Struct. 471: 1-11, 1998.

 161.Tsai, C-J., Maizel, J. V., Jr., and Nussinov, R.: Distinguishing between sequential and non-sequentially folded proteins: Implications for folding and misfolding. Protein Science 8: 1591-1604, 1999.

 162.Chen, J-H., Le, S-Y., and Maizel, J. V.: Prediction of common secondary structures of RNAs: A genetic algorithm approach.Nucleic Acids Res. 28(4): 991-999, 2000.

 163.Chen, S-L., Le, S-Y., Newton, D. L., Maizel, J. V., Jr., and Rybak, S. M.: A gender specific mRNA encoding a cytotocix ribonuclease contains a 3'UTR of unusual length and structure. Nucleic Acis Res. 28(12): 2375-2382, 2000.
 

Figure: Atomic model of a HIV rev-response element core.