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Daisuke Kihara Publications


Yang, Y. D., Park, C., Kihara, D. 2008. Threading without optimizing weighting factors for scoring function. Proteins. in press.

Hawkins, T., Chitale, M., Luban, S., Kihara, D. 2008. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins. in press. view article

Chen, H., Kihara, D. 2008. Estimating quality of template-based protein models by alignment stability. Proteins. 71: 1255-1274.

Li, B., S. Turuvekere, M. Agrawal, D. La, K. Ramani, and D. Kihara. 2008. Characterization of local geometry of protein surfaces with the visibility criterion. Proteins. 71: 670-683.

Hawkins, T., M. Chitale, and D. Kihara. 2008. New paradigm in protein function prediction for large scale omics analysis. Mol Biosyst. 4: 223-231.

Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G., Gribskov, M., Kelder, T., Kihara, D., Knight, T. F., Pico, A. R., Siegele, D. A., Wanner, B. L., Welch, R. D. 2008. The emerging world of wikis. Science. 320: 1289-1290.

Hawkins, T., Kihara, D. 2007. Function prediction of uncharacterized proteins. J Bioinform Comput Biol. 5: 1-30.

Luban, S., Kihara, D. 2007. Comparative genomics of small RNAs in bacterial genomes. Omics-a Journal of Integrative Biology. 11: 58-73.

Kihara, D., T. Hawkins, S. Luban, B. Li, K. Ramani, and M. Agrawal. 2007. Protein function prediction in proteomics era. Frontiers Comput Sci. 143-148.

Hawkins, T., Luban, S., Kihara, D. 2006. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci. 15: 1550-1556.

Hu, J., Yang, Y. D., Kihara, D. 2006. EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinformatics. 7: 342.

Kihara, D., Yang, Y. D., Hawkins, T. 2006. Bioinfornatics resources for cancer research with an emphasis in gene function and structure prediction tools. Cancer Informatics. 2: 25-35.

Tan, Y. H., Huang, H., Kihara, D. 2006. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins. 64: 587-600.

Hu, J., Li, B., Kihara, D. 2005. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res. 33: 4899-4913.

Kihara, D. 2005. The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci. 14: 1955-1963.

Kihara, D., Skolnick, J. 2004. Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins. 55: 464-473.

Skolnick, J., Kihara, D., Zhang, Y. 2004. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins. 56: 502-518.

Turuvekere, S. S., Agrawal, M., Kihara, D., Ramani, K. 2004. Feature recognition based identification of potential binding sites on the molecular surfaces. Protein Science. 13: 68-68.

Kihara, D., Skolnick, J. 2003. The PDB is a covering set of small protein structures. J Mol Biol. 334: 793-802.

Li, W., Zhang, Y., Kihara, D., Huang, Y. J., Zheng, D., Montelione, G. T., Kolinski, A., Skolnick, J. 2003. TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins. 53: 290-306.

Skolnick, J., Zhang, Y., Arakaki, A. K., Kolinski, A., Boniecki, M., Szilagyi, A., Kihara, D. 2003. TOUCHSTONE: a unified approach to protein structure prediction. Proteins. 53 Suppl 6: 469-479.

Kihara, D., Zhang, Y., Lu, H., Kolinski, A., Skolnick, J. 2002. Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A. 99: 5993-5998.

Zhang, Y., Kihara, D., Skolnick, J. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48: 192-201.

Kihara, D. 2001. Genome databases on the Internet. Tanpakushitsu Kakusan Koso. 46: 2639-2645.

Kihara, D., Lu, H., Kolinski, A., Skolnick, J. 2001. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci U S A. 98: 10125-10130.

Kolinski, A., Betancourt, M. R., Kihara, D., Rotkiewicz, P., Skolnick, J. 2001. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins. 44: 133-149.

Skolnick, J., Kihara, D. 2001. Defrosting the frozen approximation: PROSPECTOR--a new approach to threading. Proteins. 42: 319-331.

Skolnick, J., Kolinski, A., Kihara, D., Betancourt, M., Rotkiewicz, P., Boniecki, M. 2001. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins. Suppl 5: 149-156.

Kihara, D., Kanehisa, M. 2000. Tandem clusters of membrane proteins in complete genome sequences. Genome Res. 10: 731-743.

Kihara, D., Shimizu, T., Kanehisa, M. 1998. Prediction of membrane proteins based on classification of transmembrane segments. Protein Eng. 11: 961-970.

Kihara, D., Kanehisa, M., Takagi, T. 1997. Internet resources for genome research. Tanpakushitsu Kakusan Koso. 42: 3090-3099.


Sael, L., Li, B., La, D., Fang, Y., Ramani, K., Rustamov, R., Kihara, D. 2008. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins. in press.


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