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TOPSCAN specifications


Unique identifier OMICS_14542
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


  • person_outline Andrew Martin

Publication for TOPSCAN

TOPSCAN citations


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

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 […]


Efficient protein alignment algorithm for protein search

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 […]


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

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 […]


Connectivity independent protein structure alignment: a hierarchical approach

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 […]


Protein structure database search and evolutionary classification

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 […]


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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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