Publications


[95] Hyung-Rae Kim & Daisuke Kihara, Detecting local residue environment similarity for recognizing near-native structure models. Proteins: Structure, Function, and Bioinformatics, in press (2014)
[94] [Abstract] Anna T. Olek, Catherine Rayon, Lee Makowski, Hyung Rae Kim, Peter Ciesielski, John Badger, Lake N. Paul, Subhangi Ghosh, Daisuke Kihara, Michael Crowley, Michael E. Himmel, Jeffrey T. Bolin, & Nicholas C. Carpita, The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers. Plant Cell, in press (2014)
[93] [PDF] [Abstract] Atilla Sit & Daisuke Kihara, Comparison of Image Patches Using Local Moment Invariants. IEEE Transactions on Image Processing, 23: 2369-2379 (2014)
[92] [Abstract] Lenna X. Peterson, Xuejiao Kang, & Daisuke Kihara, Assessment of protein side-chain conformation prediction accuracy in different residue environments. Proteins: Structure, Function, and Bioinformatics, in press (2014)
[---] [PDF] [Abstract] Jim Cavalcoli, Lonnie Welch, Bruce Aronow, Sorin Draghici, & Daisuke Kihara, The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. Bioinformatics, 30: 148-149 (2014)
[91] [PDF] [Abstract] Sungho Won, Min-Seok Kwon, Manuel Mattheisen, Suyeon Park, Changsoon Park, Daisuke Kihara, Sven Cichon, Roel Ophoff, Markus M. Nothen, Marcella Rietschel, Max Baur, & Christoph Lange, Efficient strategy for detecting gene x gene joint action and its application in schizophrenia. Genetic Epidemiology, 38: 60-71 (2014)
[90] [PDF] [Abstract] Juan Esquivel-Rodriguez, Vianney Filos-Gonzalez, Bin Li, & Daisuke Kihara, Pairwise and multimeric protein-protein docking using the LZerD program suite. Methods in Molecular Biology, 1137: 209-234 (2014)
[89] [PDF] [Abstract] Yi Xiong, Juan Esquivel-Rodriguez, Lee Sael, & Daisuke Kihara, 3D-SURFER 2.0. Web platform for real-time search and characterization of protein surfaces. Methods in Molecular Biology, 1137: 105-117 (2014)
[88] [PDF] [Abstract] Yi Xiong, Dan Syzmanski, & Daisuke Kihara, Characterization and prediction of human protein-protein interactions. Biological Data Mining and Its Applications in Healthcare, X.-L. Li, S.-K. Ng, & J.T.L. Wang (eds), Chapter 9, pp.237-261, World Scientific, New Jersey, USA (2014)
[87] [PDF] [Abstract] Victor Padilla-Sanchez, Song Gao, Hyung Rae Kim, Daisuke Kihara, Lei Sun, Michael G Rossmann, & Venigalla B Rao, Structure-Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine. J. Mol. Biology, 426: 1019-1038(2013)
[86] [PDF] [Abstract] Juan Esquivel-Rodriguez & Daisuke Kihara, Computational methods for constructing protein structure models from 3D electron microscopy maps. J. Structural Biology, 184: 93-102 (2013)
[85] [PDF] [Abstract] Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Kilambi KP, Gray JJ, Popov P, Grudinin S, Esquivel-Rodriguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D., Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Proteins, 81: 1980-1987 (2013)
[84] [PDF] [Abstract] Yi Xiong*, Xiaolei Zhu*, & Daisuke Kihara (*Equal contribution), Ligand binding site identification. In silico Drug Discovery and Design Techniques. M. Lill (eds), Future Science, London, UK, Chapter 16, pp. 204-220 (2013)
[83] [PDF] [Abstract] Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Toronen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Honigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Bjorne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bosnjak M, Panov P, Dzeroski S, Smuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I , A large-scale evaluation of computational protein function prediction. Nature Methods, 10: 221-227(2013)
[82] [PDF] [Abstract] Meghana Chitale*, Ishita K. Khan*, & Daisuke Kihara (* equal contribution), In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. BMC Bioinformatics, 14 Suppl 3: S2 (2013)
[81] [PDF] [Abstract] David La, Misun Kong, William Hoffman, YounIm Choi & Daisuke Kihara, Predicting permanent and transient protein-protein interfaces. Proteins: Structure, Function, and Bioinformatics, 81: 805-818 (2013) [BindML+ server]
[80] [PDF] [Abstract] Chao Yuan, Hao Chen, & Daisuke Kihara, Effective inter-residue contact definitions for accurate protein fold recognition. BMC Bioinformatics, 13: 292 (2012)
[79] [PDF] [Abstract] Juan Esquivel-Rodriguez, & Daisuke Kihara, Effect of conformation sampling strategies in genetic algorithm for multiple protein docking. BMC Proceedings, 6 Suppl 7: S4 (2012)
[78] [PDF] [Abstract] Ishita Khan, Meghana Chitale, Catherine Rayon, & Daisuke Kihara, Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. BMC Proceedings, 6 Suppl 7: S5 (2012)
[77] [PDF] [Abstract] Mario Abdel Messih, Meghana Chitale, Vladimir B. Bajic, Daisuke Kihara*, & Xin Gao* (* co-corresponding authors), Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics, 28: i440-i450 (2012)
[76] [PDF] [Abstract] Juan Esquivel-Rodriguez, Yifeng D. Yang, & Daisuke Kihara , Multi-LZerD: Multiple protein docking for asymmetric complexes. Proteins: Structure, Function, and Bioinformatics, 80: 1818-1833 (2012)
[75] [PDF] [Abstract] Juan Esquivel-Rodriguez & Daisuke Kihara , Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. J Phys Chem B, 116: 6854-6861 (2012)
[74] [PDF] [Abstract] Elwood A. Mullins,Courtney M. Starks, Julie A. Francois, Lee Sael, Daisuke Kihara, & T. Joseph Kappock, Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability. Protein Science, 21: 686-696(2012)
[73] [PDF] [Abstract] Michal Jamroz, Andrzej Kolinski, & Daisuke Kihara , Structural features that predict real-value fluctuations of globular proteins. Proteins: Structure, Function, and Bioinformatics, 80: 1425-1435 (2012) [flexPred server]
[72] [PDF] [Abstract] Lee Sael*, Meghana Chitale*, & Daisuke Kihara (* equal contribution), Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics, 13: 111-123 (2012)
[71] [PDF] [Abstract] Bin Li & Daisuke Kihara , Protein Docking Prediction Using Predicted Protein-Protein Interface . BMC Bioinformatics, 13:7 (2012) [PI-LZerD software]
[70] [PDF] [Abstract] Lee Sael & Daisuke Kihara , Detecting Local Ligand-Binding Site Similarity in Non-Homologous Proteins by Surface Patch Comparison , Proteins: Str. Funct. Bioinformatics, 80: 1177-1195 (2012)
[69] [PDF] [Abstract] Juan Esquivel-Rodriguez & Daisuke Kihara , Evaluation of multiple protein docking structures using correctly predicted pairwise subunits , BMC Bioinformatics, 13:S6 (2012) (Best paper award at GLBIO 2011, ISMB )
[68] [PDF] [Abstract] Lee Sael & Daisuke Kihara , Constructing patch-based ligand-binding pocket database for predicting function of proteins, BMC Bioinformatics, 13:S7(2012)
[67] [PDF] [Abstract] Mingjie Tang*, Kean Ming Tan*, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodriguez, & Daisuke Kihara (* equal contribution), Graphical models for protein function and structure predictions., Handbook of Biological Knowledge Discovery, Mourad Elloumi & Albert Y. Zomaya(eds.), Wiley, in press (2012)
[66] [PDF] [Abstract] David La & Daisuke Kihara, A novel method for protein-protein interaction site prediction using phylogenetic substitution models., Proteins: Structure, Function, and Bioinformatics, 1: 126-141 (2012) [BindML server]
[65] [PDF] [Abstract] Zhonglian Huang, Priyanka Surana, Daisuke Kihara, Richard Meilan, & Keith Woeste, JnCML-like, an EF-hand motif-containing gene seasonally upregulated in the transition zone of black walnut (Juglans nigra L.)., American Journal of Molecular Biology, 1: 140-155 (2011)
[64] [PDF] [Abstract] Meghana Chitale, Shriphani Palakodety & Daisuke Kihara, Quantification of protein group coherence and pathway assignment using functional association., BMC Bioinformatics, 12:373 (2011)
[63] [PDF] [Abstract] SJ Fleishman, TA Whitehead, E-M Strauch, JE Corn, S Qin, H-X Zhou, JC Mitchell, ONA Demerdash, M Takeda-Shitaka, G Terashi, IH Moal, X Li, PA Bates, M Zacharias, H Park, J-S Ko, H Lee, C Seok, T Bourquard, J Bernauer, A Poupon, J Aze, S Soner, SK Ovali, P Ozbek, NB Tal, T Haliloglu, H Hwang, T Vreven, BG Pierce, Z Weng, L Perez-Cano, C Pons, J Fernandez-Recio, F Jiang, CH Robert, M Guharoy, S Liu, Y Huang, L Li, D Guo, Y Chen, Y Xiao, N London, Z Itzhaki, O Schueler-Furman, Y Inbar, V Patapov, M Cohen, G Schreiber, Y Tsuchiya, E Kanamori, DM Standley,H Nakamura, K Kinoshita, CM Driggers, RG Hall, JL Morgan, VL Hsu, J Zhan, Y Yang, Y Zhou, PL Kastritis, AMJJ Bonvin, W Zhang, CJ Camacho, KP Kilambi, B Weitzner, J Porter, A Sircar, JJ Gray, M Ohue, N Uchikoga, Y Matsuzaki, T Ishida, Y Akiyama, R Khashan, S Bush, D Fouches, A Tropsha, J Esquivel-Rodriguez, D Kihara, PB Stranges, R Jacak, B Kuhlman, SJ Wodak, J Janin, & D Baker, Community wide asssessment of protein-interface modeling using a protein design based benchmark., J. Mol. Biol, 414: 289-302(2011)
[62] [PDF] [Abstract] Daisuke Kihara, Lee Sael, Rayan Chikhi, & Juan Esquivel-Rodriguez, Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking., Curr. Protein and Peptide Science, 12: 520-530 (2011)
[61] [PDF] [Abstract] Greta L. Lundgaard, Natae E. Daniels, Slovenie Pyndiah, Erica K. Cassimere, Kazi M. Ahmed, Amelie Rodrigue, Daisuke Kihara, Carol Post, & Daitoku Sakamuro, Identification of a novel effector domain of BIN1 for cancer suppression., J. Cellular Biochemistry, 112: 2992-3001 (2011)
[60] [PDF] [Abstract] Balamurugan Jagadeesan, Amy E. Fleishman Littlejohn, Mary Anne Amalaradjou, Atul K. Singh, Krishna K. Mishra, David La, Daisuke Kihara, & Arun K. Bhunia, N-terminal Gly224-Gly411 Domain in Listeria Adhesion Protein Interacts with Host Receptor Hsp60., PLoS ONE, 6:e20694 (2011)
[59] [PDF] [Abstract] Pei-Fen Liu, Daisuke Kihara, & Chiwook Park, Energetics-based discovery of protein-ligand interactions on a proteomics scale., J. Mol. Biol., 408: 147-162 (2011)
[58] [PDF] [Abstract] Meghana Chitale & Daisuke Kihara , Computational protein function prediction: Framework and challenges., Protein function prediction for omics era, D. Kihara ed., Chapter 1, pp. 1-17, Springer. (2011)
[57] [PDF] [Abstract] Meghana Chitale & Daisuke Kihara , Enhanced sequence-based function prediction methods and application to functional similairty networks., Protein function prediction for omics era, D. Kihara ed., Chapter 2, pp. 19-34, Springer.(2011)
[56] [PDF] [Abstract] Rayan Chikhi, Lee Sael, & Daisuke Kihara , Protein binding ligand prediction using moment-based methods., Protein function prediction for omics era, D. Kihara ed., Chapter 8, pp. 145-163, Springer. (2011)
[55] [PDF] [Abstract] Hao Chen & Daisuke Kihara , Effect of using suboptimal alignments in template-based protein structure prediction., Proteins: Str. Funct. Bioinformatics, 79: 315-334. (2011) SUPRB threading program
[54] [PDF] [Abstract] Lee Sael & Daisuke Kihara , Binding ligand prediction for proteins using partial matching of local surface patches., International Journal of Molecular Sciences, 11:5009-5026. (2010)
[53] [PDF] [Abstract] Lee Sael & Daisuke Kihara, Protein surface representation for application to comparing low-resolution protein structure data., BMC Bioinformatics 11:S2. (2010) (Best Paper Award at GIW2010 )
[---] [PDF] Daisuke Kihara, Letter from Abroad: Research activity in Kihara Lab at Purdue University, Seibutsu Butsuri (Biophysics), (in Japanese) 50: 258-259, (2010).
[52] [PDF] [Abstract] Yifeng D Yang, Preston Spratt, Hao Chen, Changsoon Park & Daisuke Kihara, Sub-AQUA: Real-Value Quality Assessment of Protein Structure Models., PEDS Protein Engineering Design & Selection, 23: 617-632.(2010). [Sub-AQUA server]
[51] [PDF] [Abstract] Troy Hawkins*, Meghana Chitale* & Daisuke Kihara (* equal contribution), Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP., BMC Bioinformatics, 11:265.(2010).
[50] [PDF] [Abstract] Rayan Chikhi, Lee Sael & Daisuke Kihara, Real-time ligand binding pocket database search using local surface descriptors., Proteins: Structure, Function, and Bioinformatics, 78:2007-2028.(2010).
[49] [Abstract] Daisuke Kihara, Yifeng D Yang, & Hao Chen, Error estimation of template-based protein structure models. , Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies. Andrzej Kolinski (ed.) , Springer-Verlag, Chapter 13, pp.295-314. (2010).
[48] [PDF] [Abstract] Lee Sael & Daisuke Kihara, Characterization and classification of local protein surfaces using self-organizing map, International Journal of Knowledge Discovery in Bioinformatics, 1, 32-47.(2010).
[47] [PDF] [Abstract] Vishwesh Venkatraman, Padmasini R Chakravarthy & Daisuke Kihara, Application of 3D Zernike descriptors to shape-based ligand similarity searching, J. Cheminformatics, 1:19(2009).
[46] [PDF] [Abstract] Vishwesh Venkatraman, Yifeng D Yang, Lee Sael & Daisuke Kihara, Protein-protein docking using region-based 3D Zernike descriptors, BMC Bioinformatics, 10:407(2009). [Suppl. Data]
[45] [PDF] [Abstract] David La*, Juan Esquivel-Rodriguez*, Vishwesh Venkatraman, Bin Li, Lee Sael, Steven Ueng, Steven Ahrendt & Daisuke Kihara (* equal contribution), 3D-SURFER: software for high throughput surface comparison and analysis, Bioinformatics, 25: 2843-2844 (2009).
[44] [PDF] [Abstract] Vishwesh Venkatraman, Lee Sael & Daisuke Kihara, Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors, Cell Biochemistry and Biophysics 54: 23-32 (2009).
[43] [PDF] [Abstract] Meghana Chitale, Troy Hawkins, Changsoon Park, & Daisuke Kihara, ESG: Extended similarity group method for automated protein function prediction, Bioinformatics, 25: 1739-1745(2009).
[42] [Abstract] Lee Sael & Daisuke Kihara, Protein surface representation and comparison: New approaches in structural proteomics , (a book chapter in) Biological Data Mining, J. Chen, S. Lonardi, (eds), Chapman & Hall/CRC Press, USA, Chapter 3, pp. 89-109. (2009).
[41] [PDF] [Abstract] Daisuke Kihara, Hao Chen & Yifeng Yang, Quality assessment of computational protein models, Current Protein and Peptide Science, 10: 216-228, (2009).
[40] [PDF] [Abstract] Troy Hawkins, Meghana Chitale, Stan Luban & Daisuke Kihara, PFP: Automated prediction of gene ontology functional annotations with confidence scores, Proteins: Structure, Function, and Bioinformatics, 74: 566-582, (2009).
[39] [PDF] [Abstract] Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Daisuke Kihara, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD, The emerging world of wikis, Science, 320: 1289-1290 (2008).
[38] [Abstract] David La & Daisuke Kihara, Predicting binding interfaces of protein-protein interactions, (a book chapter in) Biological Data Mining in Protein Interaction Networks, X-L Li, S.K.Ng, (eds), Chapter 5, pp. 64-79, IGI-Global, Hershey, Philadelphia, USA. (2008).
[37] [PDF] [Abstract] Lee Sael, David La, Bin Li, Raif Rustamov & Daisuke Kihara, Rapid comparison of properties on protein surface, Proteins: Structure, Function, and Bioinformatics, 73: 1-10(2008).
[36] [Abstract] Meghana Chitale, Troy Hawkins & Daisuke Kihara, Automated prediction of protein function from sequence, In Prediction of Protein Structure, Functions and Interactions, Janusz Bujnicki (ed.), Chapter 3, pp. 64-86, John Wiley & Sons, Ltd. (2008).
[35] [PDF] [Abstract] Yifeng D. Yang, Changsoon Park & Daisuke Kihara, Threading without optimizing weighting factors for scoring function, Proteins: Structure, Function, and Bioinformatics, 73: 581-596.(2008).
[34] [PDF] [Abstract] Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov & Daisuke Kihara, Fast protein tertiary structure retrieval based on global surface shape similarity, Proteins: Structure, Function, and Bioinformatics, 72: 1259-1273. (2008).
[33] [PDF] Luo Si, Danni Yu, Daisuke Kihara, & Yi Fang, Combining gene sequence similarity and textual information for gene function annotation in the literature., Information Retrieval, 11: 389-404(2008).
[32] [PDF] [ABSTRACT] Troy Hawkins, Meghana Chitale & Daisuke Kihara, New paradigm in protein function prediction for large scale omics analysis., Molecular BioSystems, 4: 223-231 (2008).
[31] [PDF] [ABSTRACT] Hao Chen & Daisuke Kihara, Estimating quality of template-based protein models by alignment stability., Proteins: Struct. Funct. Bioinformatics, 71: 1255-1274 (2008).
[30] [PDF] [ABSTRACT] Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani & Daisuke Kihara, Characterization of local geometry of protein surfaces with the visibility criterion, Proteins: Struct. Funct. Bioinformatics, 71: 670-683 (2008).
[29] [PDF] Mingwu Zhang, Daisuke Kihara & Sunil Prabhakar, Tracing lineage in multi-version scientific databases., IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE), 440-447 (2007).
[28] [PDF] Yu-Shen Liu, Min Liu, Daisuke Kihara & Karthik Ramani, Salient critical points for meshes. , Proceedings of the 2007 ACM Solid and Physical Modeling, 277-282 (2007).
[27] [PDF] [ABSTRACT] Stan Luban & Daisuke Kihara, Comparative genomics of small RNAs in bacterial genomes, Omics, 11: 58-73 (2007).
[26] [PDF] [ABSTRACT] Troy Hawkins & Daisuke Kihara, Function prediction of uncharacterized proteins, J. Bioinformatics and Computational Biology, 5:1-30 (2007).
[25] [PDF] Daisuke Kihara, Troy Hawkins, Stan Luban Bin Li, Karthik Ramani, & Manish Agrawal, Protein function prediction in Proteomics Era" , Proceedings of the International Symposium on Frontiers of Computational Science, Y Kaneda et al. eds., pp. 143-148, Springer-Verlag, Berlin, Heidelberg. (2007).
[24] [PDF] [ABSTRACT] Jianjun Hu, Yifeng David Yang & Daisuke Kihara, EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, BMC Bioinformatics, 7:342. (2006).
[23] [PDF] [ABSTRACT] Yen Hock Tan, He Huang & Daisuke Kihara, Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences, Proteins: Structure Funct, Bioinformatics, 64: 587-600. (2006).
[22] [PDF] [ABSTRACT] Troy Hawkins, Stan Luban & Daisuke Kihara, Enhanced automated function prediction using distantly related sequences and contextual association by PFP." , Protein Sci, 15:1550-1556 (2006).
[21] [PDF] [ABSTRACT] Daisuke Kihara, Yifeng D. Yang & & Troy Hawkins, "Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools." , Cancer Informatics, 2:25-35. (2006).
[20] [PDF] [ABSTRACT] Jianjun Hu, Bin Li & Daisuke Kihara, "Limitations and potentials of current motif discovery algorithms." , Nucleic Acid Res. 33: 4899-4913. (2005).
[19] [PDF] [ABSTRACT] Daisuke Kihara., "On the effect of long-range interactions on the secondary structure formation of proteins." , Protein Science. 14: 1955-1963. (2005).
[18] [ABSTRACT] Daisuke Kihara., "Biomolecular Structure Databases." , Genome Function Research Handbook, Chapter 2. pp. 73-81. Yodosha Publishers, Tokyo, Japan. (2004).
[17] [PDF] [ABSTRACT] Jeffrey Skolnick, Daisuke Kihara and Yang Zhang., " Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm." , Proteins: Structure, Funct. Bioinformatics 56:502-518. (2004)
[16] [PDF] [ABSTRACT] Daisuke Kihara and Jeffrey Skolnick., " Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q." , Proteins: Structure, Funct. Bioinformatics 55: 464-473 (2004)
[15] [PDF] [ABSTRACT] Daisuke Kihara and Jeffrey Skolnick., " The PDB is a covering set of small protein structures." , J. Mol. Biol. 334: 793-802 (2003)
[14] [PDF] [ABSTRACT] Jeffrey Skolnick, Yang Zhang, Adrian Arakaki, Andrzej Kolinski, Michael Boniecki, Andras Szilagyi and Daisuke Kihara., " TOUCHSTONE: a unified approach to protein structure prediction." , Proteins: Structure, Funct. Genet. 53: Suppl.6: 469-479 (2003)
[13] [PDF] [ABSTRACT] Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng J. Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, and Jeffrey Skolnick, " TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data." , Proteins: Structure, Funct. Genet. 53: 290-306 (2003)
[12] [PDF] [ABSTRACT] Yang, Zhang, Daisuke Kihara and Jeffrey Skolnick, " Local Energy Landscape Flattening: Parallel Hyperbolic Monte Carlo Sampling of Protein Folding." , Proteins: Structure, Funct. Genet. 48: 192-201 (2002)
[11] [PDF] [ABSTRACT] Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, " Ab initio Protein Structure Prediction on a Genomic Scale: Application to the Mycoplasma genitalium Genome." , Proc. Natl. Acad. Sci. USA, 99: 5993-5998 (2002)
[10] [PDF] [ABSTRACT] Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr Rotkiewicz and Michael Boniecki, " Ab initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure Refinement." , Proteins: Structure, Funct. Genet. 45 (Suppl 5): 149-156 (2001)
[9] [ABSTRACT] Daisuke Kihara, " Genome Databases on the Internet." , Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme) 46 (16 Suppl): 2639-2645 (2001)
[8] [PDF] Daisuke Kihara and Minoru Kanehisa, " Prediction of Membrane Proteins in Post-Genomic Era." , Recent Res. Developments in Protein Engng. 1: 179-196 (2001)
[7] [PDF] [ABSTRACT] Daisuke Kihara, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, " TOUCHSTONE: An ab initio Protein Structure Prediction Method that Uses Threading-based Tertiary Restraints." , Proc. Natl. Acad. Sci. USA 98: 10125-10130 (2001)
[6] [PDF] [ABSTRACT] Andrzej Kolinski, Marcos Betancourt, Daisuke Kihara, Piotr Rotkiewicz and Jeffrey Skolnick, " Generalized Comparative Modeling (GENCOMP): A Combination of Sequence Comparison, Threading, and Lattice Modeling for Protein Structure Prediction and Refinement." , Proteins: Structure, Funct. Genet. 44: 133-149 (2001)
[5] [PDF] [ABSTRACT] Jeffrey Skolnick and Daisuke Kihara, " Defrosting the Frozen Approximation: PROSPECTOR - A New Approach to Threading." , Proteins: Structure, Funct. Genet. 42: 319-331 (2001)
[4] [PDF] [ABSTRACT] Daisuke Kihara and Minoru Kanehisa, " Tandem Cluster of Membrane Proteins in Complete Genome Sequences." , Genome Res. 10: 731-743 (2000)
[3] [ABSTRACT] Daisuke Kihara and Minoru Kanehisa., " The Genome Projects and Bioinformatics." , Iwanami Kouza (Iwanami Lecture Series): Gendai Igaku no Kiso (The Basis of Modern Medical Science), vol.1, Chap.11, pp: 215-235, Iwanami Shoten Publishers, Tokyo Japan (1998)
[2] [PDF] [ABSTRACT] Daisuke Kihara, Toshio Shimizu and Minoru Kanehisa, " Prediction of Membrane Proteins Based on Classification of Transmembrane Segments." , Protein Engng., 11: 961-970 (1998)
[1] [ABSTRACT] Daisuke Kihara, Minoru Kanehisa and Toshihisa Takagi., " Internet Resources for Genome Research." , Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme), 42(17 Suppl): 3090-3099 (1997)

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