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Items: 1 to 20 of 96

1.

Prediction of homo- and hetero-protein 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.

Proteins. 2016 Apr 28. doi: 10.1002/prot.25007. [Epub ahead of print]

PMID:
27122118
2.

Energetic Coupling between Ligand Binding and Dimerization in Escherichia coli Phosphoglycerate Mutase.

Gardner NW, Monroe LK, Kihara D, Park C.

Biochemistry. 2016 Mar 29;55(12):1711-23. doi: 10.1021/acs.biochem.5b00980. Epub 2016 Mar 10.

PMID:
26919584
3.

Computational protein function predictions.

Kihara D.

Methods. 2016 Jan 15;93:1-2. doi: 10.1016/j.ymeth.2016.01.001. No abstract available.

PMID:
26778120
4.

Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014.

Zhu X, Shin WH, Kim H, Kihara D.

J Chem Inf Model. 2015 Dec 30. [Epub ahead of print]

PMID:
26691286
5.

PatchSurfers: Two methods for local molecular property-based binding ligand prediction.

Shin WH, Bures MG, Kihara D.

Methods. 2016 Jan 15;93:41-50. doi: 10.1016/j.ymeth.2015.09.026. Epub 2015 Sep 30.

PMID:
26427548
6.

IAS: Interaction specific GO term associations for predicting protein-protein interaction networks.

Yerneni S, Khan I, Wei Q, Kihara D.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep 25. [Epub ahead of print]

PMID:
26415209
7.

The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches.

Khan IK, Wei Q, Chapman S, Kc DB, Kihara D.

Gigascience. 2015 Sep 14;4:43. doi: 10.1186/s13742-015-0083-4. eCollection 2015.

8.

Protein structure prediction using residue- and fragment-environment potentials in CASP11.

Kim H, Kihara D.

Proteins. 2015 Sep 7. doi: 10.1002/prot.24920. [Epub ahead of print]

PMID:
26344195
9.

Three-dimensional compound comparison methods and their application in drug discovery.

Shin WH, Zhu X, Bures MG, Kihara D.

Molecules. 2015 Jul 16;20(7):12841-62. doi: 10.3390/molecules200712841.

10.

Tuning of Pectin Methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 MODULATES THE PROCESSIVE ACTIVITY OF CO-EXPRESSED PECTIN METHYLESTERASE 3 IN A pH-DEPENDENT MANNER.

Sénéchal F, L'Enfant M, Domon JM, Rosiau E, Crépeau MJ, Surcouf O, Esquivel-Rodriguez J, Marcelo P, Mareck A, Guérineau F, Kim HR, Mravec J, Bonnin E, Jamet E, Kihara D, Lerouge P, Ralet MC, Pelloux J, Rayon C.

J Biol Chem. 2015 Sep 18;290(38):23320-35. doi: 10.1074/jbc.M115.639534. Epub 2015 Jul 16.

PMID:
26183897
11.

Navigating 3D electron microscopy maps with EM-SURFER.

Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.

BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.

12.

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.

13.

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.

14.

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;9:30. doi: 10.1186/s13062-014-0030-9.

15.

Computational characterization of moonlighting proteins.

Khan IK, Kihara D.

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

PMID:
25399606
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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