Email: [email protected]

1994 B.S.,  Biochemistry, The University of Tokyo, Japan

1. Quantification of protein group coherence and pathway assignment using functional association. M. Chitale, S. Palakodety, & D. Kihara BMC Bioinformatics, 12: 373 (2011)
2. Identification of a novel effector domain of BIN1 for cancer suppression.
3. G.L. Lundgaard, N.E. Daniels, S. Pyndiah, E.K. Cassimere, K.M. Ahmed, A. Rodrigue, D. Kihara, C. Post, & D. Sakamuro J. Cell. Biochem. 112: 2992-3001. (2011)
4. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.D. Kihara, L. Sael, R. Chikhi, J. Esquivel-Rodriguez
5. Curr. Protein and Peptide Science, 12: 520-530 (2011)
6. Energetics-based discovery of protein-ligand interactions on a proteomics scale. Pei-Fen Liu, Daisuke Kihara & Chiwook Park J. Mol. Biol, 408: 147-162 (2011)
7. Protein binding ligand prediction using moment-based methods. Rayan Chikhi, Lee Sael & Daisuke Kihara in Protein function prediction for omics era, Daisuke Kihara ed., Chapter 8, Springer-Verlag, Chap. 8, pp. 145-163. (2011)
8. Enhanced sequence-based function prediction methods and application to functional similarity networks. Meghana Chitale & Daisuke Kihara in Protein function prediction for omics era, Daisuke Kihara ed., Chapter 2, Springer-Verlag, Chap. 2, pp. 19-34. (2011)
9. Computational protein function prediction: framework and challenges. Meghana Chitale & Daisuke Kihara in Protein function prediction for omics era, Daisuke Kihara ed., Chapter 1, Springer-Verlag, Chap. 1, pp. 1-17, (2011)
10. Effect of using suboptimal alignments in template-based protein structure prediction H. Chen, & D. Kihara Proteins: Structure, Function, and Bioinformatics, 79: 315-334 (2011)
11. Binding ligand prediction for proteins using partial matching of local surface patches. Lee Sael & Daisuke Kihara Int. J. Molecular Sciences, 11: 5009-5026 (2010)
12. Protein surface representation for application to comparing low-resolution protein structure data. L. Sael, & D. Kihara BMC Bioinformatics 11: S2 (2010)
13. SubAQUA: Real-value quality assessment of protein structure models. Yifeng D.Yang, Preston Spratt, Hao Chen, Changsoon Park, & Daisuke Kihara Protein Engineering Design & Selection, 23: 617-632 (2010)
14. Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. Troy Hawkins, Meghana Chitale, & Daisuke Kihara BMC Bioinformatics, 11: 265 (2010)
15. Real-time ligand binding pocket database search using local surface descriptors. Rayan Chikhi, Lee Sael, & Daisuke Kihara Proteins: Structure, Function, and Bioinformatics, 78: 2007-2028, (2010)
16. Application of 3D Zernike descriptors to shape-based ligand similarity searching. Vishwesh Venkatraman, Padmasini R. Chakravarthy & D. Kihara J. Cheminformatics, 1: 19. (2009)
17. Protein-protein docking using region-based 3D Zernike descriptors. Viswesh Venkatraman, Yifeng D. Yang, Lee Sael & Daisuke Kihara BMC Bioinformatics, 10: 407. (2009)
18. Error estimation of template-based protein structure models. Daisuke Kihara, Yifeng D. Yang & Hao Chen Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies. Andrzej Kolinski ed., Springer-Verlag, Chapter 13, pp. 295-314. (2010)
19. 3D-SURFER: software for high throughput protein surface comparison and analysis.David La, Juan Esquivel-Rodriguez, V. Venkatraman, B. Li, L. Sael, S. Ueng, S. Ahrendt & Daisuke Kihara Bioinformatics, 25: 2843-2844. (2009)
20. Characterization and classification of local protein surfaces using self-organizing map. Lee Sael & Daisuke Kihara International Journal of Knowledge Discovery in Bioinformatics, in press. (2010)
21. Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. Vishwesh Venkatraman, Lee Sael, & Daisuke Kihara Cell Biochemistry and Biophysics, 54: 23-32(2009)
22. ESG: Extended similarity group method for automated protein function prediction. Meghana Chitale, Troy Hawkins, Changsoon Park & Daisuke Kihara Bioinformatics, 25: 1739-1745. (2009)
23. Protein surface representation and comparison: New approaches in structural proteomics. Lee Sael & Daisuke Kihara Biological Data Mining, J. Chen and S. Lonardi (eds). V. Kumar, (series ed.), Chapman & Hall/CRC Press, Boca Raton, Florida, USA, Chapter 3, pp. 89-109. (2009)
24. Quality assessment of protein structure models. Daisuke Kihara, Hao Chen & Yifeng D. Yang Current Protein and Peptide Science, 10: 216-228 (2009)
25. Predicting binding interfaces of protein-protein interactions. David La & Daisuke Kihara. Biological Data Mining in Protein Interaction -etworks, X.-L. Li and S.K. Ng (eds), Chapter 5, pp. 64-79, IGI-Global, Hershey, Philadelphia, USA. (2009)
26. The emerging world of wikis. Hu, J. C., R. Aramayo, D. Bolser, T. Conway, C. G. Elsik, M. Gribskov, T. Kelder, D. Kihara, T. F. Knight, Jr., A. R. Pico, D. A. Siegele, B. L. Wanner, and R. D. Welch. Science 320 (5881):1289-1290, (2008)
27. PFP: Automated prediction of gene ontology function annotations with confidence scores. Troy Hawkins, Meghana Chitale, Stan Luban & Daisuke Kihara Proteins: Structure, Function, and Bioinformatics, 74: 566-582, (2009).
28. Automated prediction of protein function from sequence. Meghana Chitale, Troy Hawkins & Daisuke Kihara Prediction of Protein Structure, Functions and Interactions, Janusz Bujnicki (ed.), Chapter 3, pp. 64-86, John Wiley & Sons, Ltd. (2009)
29. Rapid comparison of properties on protein surface. Lee Sael, David La, Bin Li, Raif Rustamov, & Daisuke Kihara. Proteins: Structure, Function, and Bioinformatics, 73: 1-10, (2008).
30. New paradigm in protein function prediction for large scale omics analysis. Troy Hawkins, Meghana Chitale & Daisuke Kihara. Molecular BioSystems, 4: 223-231 (2008)
31. Fast protein tertiary structure retrieval based on global surface shape similarity. Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov & Daisuke Kihara. Proteins: Structure, Function, and Bioinformatics, 72: 1259-1273. (2008).
32. Combining sequence similarity scores and textual information for gene function annotation in the literature. Luo Si, D. Yu, Daisuke Kihara & F. Yi. Information Retrieval, 11: 389-404 (2008)
33. Threading without optimizing weighting factors for scoring function. Yifeng D. Yang, Changsoon Park & Daisuke Kihara. Proteins, 73:581-596, (2008)

Profile Details

https://www.bio.purdue.edu/People/profile/dkihara.html

https://www.researchgate.net/profile/Daisuke-Kihara

https://scholar.google.com/citations?user=WfGLzyAAAAAJ&hl=en