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Protocols

GalaxyTBM specifications

Information


Unique identifier OMICS_08421
Name GalaxyTBM
Interface Web user interface
Restrictions to use None
Input data A SEQ file in the FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chaok Seok

Publication for GalaxyTBM

GalaxyTBM citations

 (3)
library_books

An Escherichia coli Strain, PGB01, Isolated from Feral Pigeon Faeces, Thermally Fit to Survive in Pigeon, Shows High Level Resistance to Trimethoprim

2015
PLoS One
PMCID: 4353713
PMID: 25750990
DOI: 10.1371/journal.pone.0119329

[…] 76) using CLUSTAL W [] was done to identify the altered residues.Three-dimensional protein model of PGB01-DfrA7 (Ac.No. CBH31027) was generated by using homology modeling approach. Model was made via GalaxyTBM []. Five templates (PDB ID: 3TQ8, 1ZDR, 3DAU, 3IA4 and 3IX9) with sequence identity of 6–29% to the target were selected by the GalaxyTBM pipeline and additionally structure was refined by u […]

library_books

Molecular Characterization of msp2/p44 of Anaplasma phagocytophilum Isolated from Infected Patients and Haemaphysalis longicornis in Laizhou Bay, Shandong Province, China

2013
PLoS One
PMCID: 3805589
PMID: 24167608
DOI: 10.1371/journal.pone.0078189

[…] Protein tertiary structure prediction was performed using the program GalaxyTBM (http://galaxy.seoklab.org/), and the predicted results are shown in . The predicted results indicated that the MSP2 protein tertiary structures of the LZ-HGA-Agent isolate, the APH-HZ and t […]

call_split

GalaxyWEB server for protein structure prediction and refinement

2012
Nucleic Acids Res
PMCID: 3394311
PMID: 22649060
DOI: 10.1093/nar/gks493
call_split See protocol

[…] A flowchart of the GalaxyWEB structure prediction (GalaxyTBM) and refinement (GalaxyREFINE) procedure is shown in . First, candidates for templates are selected by rescoring HHsearch () results placing more weights on the secondary structure score for […]

Citations

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GalaxyTBM institution(s)
Department of Chemistry, Seoul National University, Seoul, Korea
GalaxyTBM funding source(s)
This work was supported by the KOSEF/MEST Grant No. 2011–0012456 and the Center for Marine Natural Products and Drug Discovery (CMDD), one of the MarineBio21 programs funded by the Ministry of Land, Transport, and Maritime Affairs.

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