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Protocols

fastSCOP specifications

Information


Unique identifier OMICS_14480
Name fastSCOP
Interface Web user interface
Restrictions to use None
Input data Query protein
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jinn-Moon Yang

Publication for fastSCOP

fastSCOP citations

 (3)
library_books

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

2014
BMC Bioinformatics
PMCID: 4032388
PMID: 24742328
DOI: 10.1186/1471-2105-15-112

[…] 1012 consists of two domains: the N-terminal (β/α)8−barrel (ΤΙΜ-barrel) domain comprising residues 27 to 370 and the C-terminal Greek-key β-sandwich domain covering residues 371 to 483, respectively. FastSCOP classification database search results confirms the TIM beta/alpha barrel fold classification of N-terminal domain shows and further identifies it as a member of the beta-glycanases SCOP supe […]

call_split

Elementary Flux Modes Analysis of Functional Domain Networks Allows a Better Metabolic Pathway Interpretation

2013
PLoS One
PMCID: 3812217
PMID: 24204596
DOI: 10.1371/journal.pone.0076143
call_split See protocol

[…] model of each enzyme is selected based on the lowest modeller objective function score (MOF). After this step, the structural domains of the proteins are assigned to each of the protein models using fastSCOP , . Besides, fastSCOP, PFAM , , Swiss-Prot and literature review were used for the functional domain assignment.We illustrate our approach on the Bacillus subtilis pyruvate dehydrogenase mul […]

library_books

Structural bioinformatics of the human spliceosomal proteome

2012
Nucleic Acids Res
PMCID: 3424538
PMID: 22573172
DOI: 10.1093/nar/gks347

[…] domain identification were either extracted from the Protein Data Bank or from the SCOP parseable files on the SCOP website (http://scop.mrc-lmb.cam.ac.uk/scop/parse/index.html) or assigned using the fastSCOP server (http://fastscop.life.nctu.edu.tw/) (). PFAM domain names were assigned on the PFAM website (http://pfam.sanger.ac.uk/). SCOP v. 1.75 and PFAM v. 25.0 were used. Structural similarity […]

Citations

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fastSCOP institution(s)
Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; National Chiao Tung University, Hsinchu, Taiwan; Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan
fastSCOP funding source(s)
This work was supported by National Science Council and partial support of the ATU plan by MOE.

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