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Results: 1 to 20 of 75

1.

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 10. pii: tpc.114.126862. [Epub ahead of print]

PMID:
25012190
[PubMed - as supplied by publisher]
Free Article
2.

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]
3.

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

Peterson LX, Kang X, Kihara D.

Proteins. 2014 Mar 12. doi: 10.1002/prot.24552. [Epub ahead of print]

PMID:
24619909
[PubMed - as supplied by publisher]
4.

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 - in process]
5.

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 - in process]
6.

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]
7.

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]
8.

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]
9.

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]
10.

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
11.

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
12.

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
13.

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
14.

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
15.

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
16.

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
17.

Constructing patch-based ligand-binding pocket database for predicting function of proteins.

Sael L, Kihara D.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S7. doi: 10.1186/1471-2105-13-S2-S7.

PMID:
22536870
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits.

Esquivel-Rodríguez J, Kihara D.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S6. doi: 10.1186/1471-2105-13-S2-S6.

PMID:
22536869
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Multi-LZerD: multiple protein docking for asymmetric complexes.

Esquivel-Rodríguez J, Yang YD, Kihara D.

Proteins. 2012 Jul;80(7):1818-33. doi: 10.1002/prot.24079. Epub 2012 May 8.

PMID:
22488467
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

Esquivel-Rodríguez J, Kihara D.

J Phys Chem B. 2012 Jun 14;116(23):6854-61. doi: 10.1021/jp212612t. Epub 2012 Mar 30.

PMID:
22417139
[PubMed - indexed for MEDLINE]
Free PMC Article

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