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Results: 1 to 20 of 79

1.

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 7. pii: tpc.114.127563. [Epub ahead of print]

PMID:
25293756
[PubMed - as supplied by publisher]
Free Article
2.

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

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

Bioinformatics. 2014 Oct 1. pii: btu646. [Epub ahead of print]

PMID:
25273111
[PubMed - as supplied by publisher]
3.

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
4.

Detecting Local Residue Environment Similarity for Recognizing Near-Native Structure Models.

Kim H, Kihara D.

Proteins. 2014 Jul 31. doi: 10.1002/prot.24658. [Epub ahead of print]

PMID:
25132526
[PubMed - as supplied by publisher]
5.

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
6.

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]
7.

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]
8.

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]
9.

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]
10.

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]
11.

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]
12.

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]
13.

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
14.

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
15.

A large-scale evaluation of computational protein function prediction.

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, Törönen 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, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc 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.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

PMID:
23353650
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Predicting permanent and transient protein-protein interfaces.

La D, Kong M, Hoffman W, Choi YI, Kihara D.

Proteins. 2013 May;81(5):805-18. doi: 10.1002/prot.24235. Epub 2013 Jan 15.

PMID:
23239312
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins.

Khan I, Chitale M, Rayon C, Kihara D.

BMC Proc. 2012 Nov 13;6 Suppl 7:S5. doi: 10.1186/1753-6561-6-S7-S5. Epub 2012 Nov 13.

PMID:
23173871
[PubMed]
Free PMC Article
18.

Effect of conformation sampling strategies in genetic algorithm for multiple protein docking.

Esquivel-Rodríguez J, Kihara D.

BMC Proc. 2012 Nov 13;6 Suppl 7:S4. doi: 10.1186/1753-6561-6-S7-S4. Epub 2012 Nov 13.

PMID:
23173833
[PubMed]
Free PMC Article
19.

Effective inter-residue contact definitions for accurate protein fold recognition.

Yuan C, Chen H, Kihara D.

BMC Bioinformatics. 2012 Nov 9;13:292. doi: 10.1186/1471-2105-13-292.

PMID:
23140471
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Protein domain recurrence and order can enhance prediction of protein functions.

Messih MA, Chitale M, Bajic VB, Kihara D, Gao X.

Bioinformatics. 2012 Sep 15;28(18):i444-i450. doi: 10.1093/bioinformatics/bts398.

PMID:
22962465
[PubMed - indexed for MEDLINE]
Free PMC Article

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