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[Genome databases on the Internet].
Kihara D. Kihara D. Tanpakushitsu Kakusan Koso. 2001 Dec;46(16 Suppl):2639-45. Tanpakushitsu Kakusan Koso. 2001. PMID: 11802444 Review. Japanese. No abstract available.
[Internet resources for genome research].
Kihara D, Kanehisa M, Takagi T. Kihara D, et al. Tanpakushitsu Kakusan Koso. 1997 Dec;42(17 Suppl):3090-9. Tanpakushitsu Kakusan Koso. 1997. PMID: 9455244 Review. Japanese. No abstract available.
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.
Skolnick J, Kolinski A, Kihara D, Betancourt M, Rotkiewicz P, Boniecki M. Skolnick J, et al. Among authors: kihara d. Proteins. 2001;Suppl 5:149-56. doi: 10.1002/prot.1172. Proteins. 2001. PMID: 11835492
Tandem clusters of membrane proteins in complete genome sequences.
Kihara D, Kanehisa M. Kihara D, et al. Genome Res. 2000 Jun;10(6):731-43. doi: 10.1101/gr.10.6.731. Genome Res. 2000. PMID: 10854407
Prediction of membrane proteins based on classification of transmembrane segments.
Kihara D, Shimizu T, Kanehisa M. Kihara D, et al. Protein Eng. 1998 Nov;11(11):961-70. doi: 10.1093/protein/11.11.961. Protein Eng. 1998. PMID: 9876916
Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.
Terashi G, Kihara D. Terashi G, et al. Among authors: kihara d. Proteins. 2018 Mar;86 Suppl 1(Suppl 1):189-201. doi: 10.1002/prot.25373. Epub 2017 Sep 1. Proteins. 2018. PMID: 28833585 Free PMC article.
Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.
Peterson LX, Kim H, Esquivel-Rodriguez J, Roy A, Han X, Shin WH, Zhang J, Terashi G, Lee M, Kihara D. Peterson LX, et al. Among authors: kihara d. Proteins. 2017 Mar;85(3):513-527. doi: 10.1002/prot.25165. Epub 2016 Oct 14. Proteins. 2017. PMID: 27654025 Free PMC article.
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Lensink MF, et al. Among authors: kihara d. Proteins. 2016 Sep;84 Suppl 1(Suppl Suppl 1):323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1. Proteins. 2016. PMID: 27122118 Free PMC article.
Detecting local residue environment similarity for recognizing near-native structure models.
Kim H, Kihara D. Kim H, et al. Among authors: kihara d. Proteins. 2014 Dec;82(12):3255-72. doi: 10.1002/prot.24658. Epub 2014 Oct 30. Proteins. 2014. PMID: 25132526 Free PMC article.
Structural features that predict real-value fluctuations of globular proteins.
Jamroz M, Kolinski A, Kihara D. Jamroz M, et al. Among authors: kihara d. Proteins. 2012 May;80(5):1425-35. doi: 10.1002/prot.24040. Epub 2012 Feb 13. Proteins. 2012. PMID: 22328193 Free PMC article.
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