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TOPSCAN specifications

Information


Unique identifier OMICS_14542
Name TOPSCAN
Interface Web user interface
Restrictions to use None
Input data Local PDB file
Input format PDB
Programming languages C, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Andrew Martin

Publication for TOPSCAN

TOPSCAN citations

 (5)
library_books

TS AMIR: a topology string alignment method for intensive rapid protein structure comparison

2012
PMCID: 3298807
PMID: 22336468
DOI: 10.1186/1748-7188-7-4

[…] FASTA [], BLAST [] or other language modelling techniques are employed to capture structural similarities among proteins. The methods include protein structure modelling in a set of topology strings (TOPSCAN) [], hidden Markov model derived structural alphabet (SA-Search) [], representing discrete internal angles of protein backbone as a sequence (YAKUSA) [], kappa-alpha (κ, α) plot derived struct […]

library_books

Efficient protein alignment algorithm for protein search

2010
BMC Bioinformatics
PMCID: 3009506
PMID: 20122207
DOI: 10.1186/1471-2105-11-S1-S34

[…] ns to do the queries on our search engine, use Q-score as the criterion to rank the output proteins, and compare the result with that of CE [], MAMMOTH [], 3D-BLAST [], PSI-BLAST [], ProtDex2 [], and TopScan []. Results for all the methods except ours are taken from []. Since our sequential method is much faster than its non-sequential counterpart, we just use the sequential method in our experime […]

library_books

Kappa alpha plot derived structural alphabet and BLOSUM like substitution matrix for rapid search of protein structure database

2007
Genome Biol
PMCID: 1868941
PMID: 17335583
DOI: 10.1186/gb-2007-8-3-r31

[…] core at least a threshold when aligned with some words within the query sequence; the algorithm then extends each such 'hit' in both directions to check the alignment score [].MAMMOTH is the best and TOPSCAN is the worst for these 108 queries among these six methods (Figure ). 3D-BLAST was much better than fast structure database search methods (TOPSCAN [] and ProtDex2 []), and its performance app […]

library_books

Connectivity independent protein structure alignment: a hierarchical approach

2006
BMC Bioinformatics
PMCID: 1683948
PMID: 17118190
DOI: 10.1186/1471-2105-7-510

[…] AP [], FASE [] and SCALI [] work on the residue level or a combination of secondary-structure and residue level. Another approach employs methods derived from computer vision to compare 3D models []. TOPSCAN [] uses topology string representations. Other approaches tackle even the problem of aligning multiple structures [,]. Theoretical work characterizing protein architectures focused initially o […]

library_books

Protein structure database search and evolutionary classification

2006
Nucleic Acids Res
PMCID: 1540718
PMID: 16885238
DOI: 10.1093/nar/gkl395

[…] () and ProteinDBS () have been proposed to search protein structures more quickly by mapping a structure into indexes for measuring the distance of two structures. Other fast search tools, including TOPSCAN (), SA-Search () and YAKUSA (), describe protein structures as 1D sequences and then use specific sequence alignment methods to align two structures. Many of these methods have been evaluated […]

Citations

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TOPSCAN institution(s)
School of Animal and Microbial Sciences, University of Reading, Whiteknights, UK
TOPSCAN funding source(s)
This work was supported by departmental funds at University College.

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