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Results: 1 to 20 of 85

1.

On the origin of protein superfamilies and superfolds.

Magner A, Szpankowski W, Kihara D.

Sci Rep. 2015 Feb 23;5:8166. doi: 10.1038/srep08166.

PMID:
25703447
[PubMed - in process]
Free PMC Article
2.

Virus structure. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children.

Liu Y, Sheng J, Fokine A, Meng G, Shin WH, Long F, Kuhn RJ, Kihara D, Rossmann MG.

Science. 2015 Jan 2;347(6217):71-4. doi: 10.1126/science.1261962.

PMID:
25554786
[PubMed - indexed for MEDLINE]
3.

Genome-scale identification and characterization of moonlighting proteins.

Khan I, Chen Y, Dong T, Hong X, Takeuchi R, Mori H, Kihara D.

Biol Direct. 2014 Dec 11;9(1):30. doi: 10.1186/s13062-014-0030-9.

PMID:
25497125
[PubMed - in process]
Free PMC Article
4.

Computational characterization of moonlighting proteins.

Khan IK, Kihara D.

Biochem Soc Trans. 2014 Dec;42(6):1780-5. doi: 10.1042/BST20140214.

PMID:
25399606
[PubMed - in process]
5.

GenoBase: comprehensive resource database of Escherichia coli K-12.

Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL, Mori H.

Nucleic Acids Res. 2015 Jan;43(Database issue):D606-17. doi: 10.1093/nar/gku1164. Epub 2014 Nov 15.

PMID:
25399415
[PubMed - in process]
Free Article
6.

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.

Zhu X, Xiong Y, Kihara D.

Bioinformatics. 2015 Mar 1;31(5):707-13. doi: 10.1093/bioinformatics/btu724. Epub 2014 Oct 29.

PMID:
25359888
[PubMed - in process]
7.

A proteomic strategy for global analysis of plant protein complexes.

Aryal UK, Xiong Y, McBride Z, Kihara D, Xie J, Hall MC, Szymanski DB.

Plant Cell. 2014 Oct;26(10):3867-82. doi: 10.1105/tpc.114.127563. Epub 2014 Oct 7.

PMID:
25293756
[PubMed - in process]
Free PMC Article
8.

PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool.

Khan IK, Wei Q, Chitale M, Kihara D.

Bioinformatics. 2015 Jan 15;31(2):271-2. doi: 10.1093/bioinformatics/btu646. Epub 2014 Oct 1.

PMID:
25273111
[PubMed - in process]
9.

PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.

Hu B, Zhu X, Monroe L, Bures MG, Kihara D.

Int J Mol Sci. 2014 Aug 27;15(9):15122-45. doi: 10.3390/ijms150915122.

PMID:
25167137
[PubMed - in process]
Free PMC Article
10.

Detecting local residue environment similarity for recognizing near-native structure models.

Kim H, Kihara D.

Proteins. 2014 Dec;82(12):3255-72. doi: 10.1002/prot.24658. Epub 2014 Oct 30.

PMID:
25132526
[PubMed - in process]
11.

The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers.

Olek AT, Rayon C, Makowski L, Kim HR, Ciesielski P, Badger J, Paul LN, Ghosh S, Kihara D, Crowley M, Himmel ME, Bolin JT, Carpita NC.

Plant Cell. 2014 Jul;26(7):2996-3009. doi: 10.1105/tpc.114.126862. Epub 2014 Jul 10.

PMID:
25012190
[PubMed - in process]
Free PMC Article
12.

Comparison of image patches using local moment invariants.

Sit A, Kihara D.

IEEE Trans Image Process. 2014 May;23(5):2369-79.

PMID:
24718574
[PubMed - in process]
13.

Assessment of protein side-chain conformation prediction methods in different residue environments.

Peterson LX, Kang X, Kihara D.

Proteins. 2014 Sep;82(9):1971-84. doi: 10.1002/prot.24552. Epub 2014 Mar 31.

PMID:
24619909
[PubMed - in process]
14.

Pairwise and multimeric protein-protein docking using the LZerD program suite.

Esquivel-Rodriguez J, Filos-Gonzalez V, Li B, Kihara D.

Methods Mol Biol. 2014;1137:209-34. doi: 10.1007/978-1-4939-0366-5_15.

PMID:
24573484
[PubMed - indexed for MEDLINE]
15.

3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

Xiong Y, Esquivel-Rodriguez J, Sael L, Kihara D.

Methods Mol Biol. 2014;1137:105-17. doi: 10.1007/978-1-4939-0366-5_8.

PMID:
24573477
[PubMed - indexed for MEDLINE]
16.

Efficient strategy for detecting gene × gene joint action and its application in schizophrenia.

Won S, Kwon MS, Mattheisen M, Park S, Park C, Kihara D, Cichon S, Ophoff R, Nöthen MM, Rietschel M, Baur M, Uitterlinden AG, Hofmann A; GROUP Investigators, Lange C.

Genet Epidemiol. 2014 Jan;38(1):60-71. doi: 10.1002/gepi.21779. Epub 2013 Nov 23.

PMID:
24272960
[PubMed - indexed for MEDLINE]
17.

Structure-function analysis of the DNA translocating portal of the bacteriophage T4 packaging machine.

Padilla-Sanchez V, Gao S, Kim HR, Kihara D, Sun L, Rossmann MG, Rao VB.

J Mol Biol. 2014 Mar 6;426(5):1019-38. doi: 10.1016/j.jmb.2013.10.011. Epub 2013 Oct 11.

PMID:
24126213
[PubMed - indexed for MEDLINE]
18.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

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, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez 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.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

PMID:
23843247
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

Esquivel-Rodríguez J, Kihara D.

J Struct Biol. 2013 Oct;184(1):93-102. doi: 10.1016/j.jsb.2013.06.008. Epub 2013 Jun 21.

PMID:
23796504
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.

Chitale M, Khan IK, Kihara D.

BMC Bioinformatics. 2013;14 Suppl 3:S2. doi: 10.1186/1471-2105-14-S3-S2. Epub 2013 Feb 28.

PMID:
23514353
[PubMed - indexed for MEDLINE]
Free PMC Article
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