Del Carpio CA - Search Results

1

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: del carpio ca. 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.

2

Molecular dynamics study on the ligand recognition by tandem SH3 domains of p47phox, regulating NADPH oxidase activity.

Watanabe Y, Tsuboi H, Koyama M, Kubo M, Del Carpio CA, Broclawik E, Ichiishi E, Kohno M, Miyamoto A. Watanabe Y, et al. Among authors: del carpio ca. Comput Biol Chem. 2006 Aug;30(4):303-12. doi: 10.1016/j.compbiolchem.2006.04.004. Epub 2006 Jun 22. Comput Biol Chem. 2006. PMID: 16798095

3

Three-dimensional quantitative structure-activity relationship (3 D-QSAR) and docking studies on (benzothiazole-2-yl) acetonitrile derivatives as c-Jun N-terminal kinase-3 (JNK3) inhibitors.

Shaikh AR, Ismael M, Del Carpio CA, Tsuboi H, Koyama M, Endou A, Kubo M, Broclawik E, Miyamoto A. Shaikh AR, et al. Among authors: del carpio ca. Bioorg Med Chem Lett. 2006 Nov 15;16(22):5917-25. doi: 10.1016/j.bmcl.2006.06.039. Epub 2006 Sep 20. Bioorg Med Chem Lett. 2006. PMID: 16989998

4

The effect of R249S carcinogenic and H168R-R249S suppressor mutations on p53-DNA interaction, a multi scale computational study.

Rauf SM, Ismael M, Sahu KK, Suzuki A, Koyama M, Tsuboi H, Hatakeyama N, Endou A, Takaba H, Del Carpio CA, Kubo M, Miyamoto A. Rauf SM, et al. Among authors: del carpio ca. Comput Biol Med. 2010 May;40(5):498-508. doi: 10.1016/j.compbiomed.2010.03.004. Epub 2010 Apr 18. Comput Biol Med. 2010. PMID: 20403587

5

Identification of amino acid residues in the Ah receptor involved in ligand binding.

Goryo K, Suzuki A, Del Carpio CA, Siizaki K, Kuriyama E, Mikami Y, Kinoshita K, Yasumoto K, Rannug A, Miyamoto A, Fujii-Kuriyama Y, Sogawa K. Goryo K, et al. Among authors: del carpio ca. Biochem Biophys Res Commun. 2007 Mar 9;354(2):396-402. doi: 10.1016/j.bbrc.2006.12.227. Epub 2007 Jan 10. Biochem Biophys Res Commun. 2007. PMID: 17227672

6

Automatic epitope recognition in proteins oriented to the system for macromolecular interaction assessment MIAX.

Yoshimori A, Del Carpio CA. Yoshimori A, et al. Among authors: del carpio ca. Genome Inform. 2001;12:113-22. Genome Inform. 2001. PMID: 11791230

7

MIAX: a system for assessment of macromolecular interaction. 3) A parallel hybrid GA for flexible protein docking.

Del Carpio CA, Yoshimori A. Del Carpio CA, et al. Genome Inform Ser Workshop Genome Inform. 2000;11:205-14. Genome Inform Ser Workshop Genome Inform. 2000. PMID: 11700601

8

Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling.

Shaikh AR, Broclawik E, Tsuboi H, Koyama M, Endou A, Takaba H, Kubo M, Del Carpio CA, Miyamoto A. Shaikh AR, et al. Among authors: del carpio ca. J Mol Model. 2007 Jul;13(6-7):851-60. doi: 10.1007/s00894-007-0196-5. Epub 2007 Mar 27. J Mol Model. 2007. PMID: 17387527

9

Robotic path planning and protein complex modeling considering low frequency intra-molecular loop and domain motions.

Del Carpio CA, Qiang P, Ichiishi E, Tsuboi H, Koyama M, Hatakeyama N, Endou A, Takaba H, Kubo M, Miyamoto A. Del Carpio CA, et al. Genome Inform. 2006;17(2):270-8. Genome Inform. 2006. PMID: 17503399

10

Tribochemical reaction dynamics of phosphoric ester lubricant additive by using a hybrid tight-binding quantum chemical molecular dynamics method.

Koyama M, Hayakawa J, Onodera T, Ito K, Tsuboi H, Endou A, Kubo M, Del Carpio CA, Miyamoto A. Koyama M, et al. Among authors: del carpio ca. J Phys Chem B. 2006 Sep 7;110(35):17507-11. doi: 10.1021/jp061210m. J Phys Chem B. 2006. PMID: 16942091

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