Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 25

1.

Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.

Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D.

Nat Methods. 2019 Sep;16(9):911-917. doi: 10.1038/s41592-019-0500-1. Epub 2019 Jul 29.

PMID:
31358979
2.

De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.

Terashi G, Kihara D.

J Struct Biol. 2018 Nov;204(2):351-359. doi: 10.1016/j.jsb.2018.07.013. Epub 2018 Jul 31.

3.

De novo main-chain modeling for EM maps using MAINMAST.

Terashi G, Kihara D.

Nat Commun. 2018 Apr 24;9(1):1618. doi: 10.1038/s41467-018-04053-7.

4.

Modeling the assembly order of multimeric heteroprotein complexes.

Peterson LX, Togawa Y, Esquivel-Rodriguez J, Terashi G, Christoffer C, Roy A, Shin WH, Kihara D.

PLoS Comput Biol. 2018 Jan 12;14(1):e1005937. doi: 10.1371/journal.pcbi.1005937. eCollection 2018 Jan.

5.

Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.

Terashi G, Kihara D.

Proteins. 2018 Mar;86 Suppl 1:189-201. doi: 10.1002/prot.25373. Epub 2017 Sep 1.

6.

Modeling disordered protein interactions from biophysical principles.

Peterson LX, Roy A, Christoffer C, Terashi G, Kihara D.

PLoS Comput Biol. 2017 Apr 10;13(4):e1005485. doi: 10.1371/journal.pcbi.1005485. eCollection 2017 Apr.

7.

Variability of Protein Structure Models from Electron Microscopy.

Monroe L, Terashi G, Kihara D.

Structure. 2017 Apr 4;25(4):592-602.e2. doi: 10.1016/j.str.2017.02.004. Epub 2017 Mar 2.

8.

Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.

Peterson LX, Kim H, Esquivel-Rodriguez J, Roy A, Han X, Shin WH, Zhang J, Terashi G, Lee M, Kihara D.

Proteins. 2017 Mar;85(3):513-527. doi: 10.1002/prot.25165. Epub 2016 Oct 14.

9.

Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor.

Nojima H, Kanou K, Terashi G, Takeda-Shitaka M, Inoue G, Atsuda K, Itoh C, Iguchi C, Matsubara H.

BMC Struct Biol. 2016 Aug 5;16:11. doi: 10.1186/s12900-016-0062-8.

10.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Terashi G, Takeda-Shitaka M.

PLoS One. 2015 Oct 26;10(10):e0141440. doi: 10.1371/journal.pone.0141440. eCollection 2015.

11.

Quality assessment methods for 3D protein structure models based on a residue-residue distance matrix prediction.

Terashi G, Nakamura Y, Shimoyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2014;62(8):744-53.

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.

13.

United3D: a protein model quality assessment program that uses two consensus based methods.

Terashi G, Oosawa M, Nakamura Y, Kanou K, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2012;60(11):1359-65.

14.

LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value.

Terashi G, Shibuya T, Takeda-Shitaka M.

J Comput Biol. 2012 May;19(5):493-503. doi: 10.1089/cmb.2011.0230. Epub 2012 Apr 17.

PMID:
22509779
15.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.

J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29.

16.

New protein structure model evaluation methods that include a side-chain consensus score for the protein modeling.

Kanou K, Hirata T, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2010 Feb;58(2):180-90.

17.

HUMAN FAMSD-BASE: high quality protein structure model database for the human genome using the FAMSD homology modeling method.

Kanou K, Hirata T, Iwadate M, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2010 Jan;58(1):66-75.

18.

Method for predicting homology modeling accuracy from amino acid sequence alignment: the power function.

Iwadate M, Kanou K, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2010 Jan;58(1):1-10.

19.

FAMSD: A powerful protein modeling platform that combines alignment methods, homology modeling, 3D structure quality estimation and molecular dynamics.

Kanou K, Iwadate M, Hirata T, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2009 Dec;57(12):1335-42.

20.

Bioinformatics based Ligand-Docking and in-silico screening.

Takaya D, Takeda-Shitaka M, Terashi G, Kanou K, Iwadate M, Umeyama H.

Chem Pharm Bull (Tokyo). 2008 May;56(5):742-4.

21.

Fams-ace: a combined method to select the best model after remodeling all server models.

Terashi G, Takeda-Shitaka M, Kanou K, Iwadate M, Takaya D, Hosoi A, Ohta K, Umeyama H.

Proteins. 2007;69 Suppl 8:98-107.

PMID:
17894329
22.

The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation.

Terashi G, Takeda-Shitaka M, Kanou K, Iwadate M, Takaya D, Umeyama H.

Proteins. 2007 Dec 1;69(4):866-72.

PMID:
17853449
23.

FAMS complex: a fully automated homology modeling system for protein complex structures.

Takeda-Shitaka M, Terashi G, Chiba C, Takaya D, Umeyama H.

Med Chem. 2006 Mar;2(2):191-201.

PMID:
16787367
24.

Protein structure prediction in CASP6 using CHIMERA and FAMS.

Takeda-Shitaka M, Terashi G, Takaya D, Kanou K, Iwadate M, Umeyama H.

Proteins. 2005;61 Suppl 7:122-7.

PMID:
16187353
25.

Supplemental Content

Loading ...
Support Center