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Protocols

Vorolign specifications

Information


Unique identifier OMICS_03661
Name Vorolign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Publication for Vorolign

Vorolign citations

 (9)
library_books

In Silico Characterization and Functional Validation of Cell Wall Modification Genes Imparting Waterlogging Tolerance in Maize

2017
Bioinform Biol Insights
PMCID: 5753887
PMID: 29317803
DOI: 10.1177/1177932217747277

[…] ronases (GRMZM2G037431) and endoglucanases (GRMZM2G141911) were observed for similar contact maps. Clustering results of ProcCKSI tools were used to assess the multiple protein structural alignments. Vorolign and URMS revealed a best clustering of arabinogalactan (GRMZM2G003165) and expansins (GRMZM2G105844). The z-score of combinatorial extension revealed the clusters of arabinogalactan (GRMZM2G0 […]

call_split

Classifying the metal dependence of uncharacterized nitrogenases

2013
Front Microbiol
PMCID: 3578447
PMID: 23440025
DOI: 10.3389/fmicb.2012.00419
call_split See protocol

[…] nferred structures were compared using an “all against all” comparison performed by the ProCKSI server. The relatedness of structures was calculated with standardized distance matrix derived from the Vorolign V-score () and hierarchical clustering accomplished using the Complete Link (furthest neighbor) method () with the Clustering Calculator server.Active site volumetric calculations were perfor […]

library_books

SProt: sphere based protein structure similarity algorithm

2011
Proteome Sci
PMCID: 3289081
PMID: 22166105
DOI: 10.1186/1477-5956-9-S1-S20

[…] imilar to the query. Accuracy of classification at a given level is measured as the percentage of correctly classified queries.We used the dataset that was originally introduced for evaluation of the Vorolign method (Vorolign dataset). The dataset utilizes ASTRAL-25 v1.65 [] containing 4,357 structures. As the query set, 979 structures from difference set between SCOP v1.67 and v1.65 are used.Resu […]

call_split

Vorescore—fold recognition improved by rescoring of protein structure models

2010
Bioinformatics
PMCID: 2935407
PMID: 20823310
DOI: 10.1093/bioinformatics/btq369
call_split See protocol

[…] th a template. The (re-)scoring of the model structure is done via comparing the two structures, the native template structure and the target model structure via a structural alignment method. We use Vorolign as it has a very high accuracy on the family (∼97%) and superfamily (∼90%) but in contrast to other methods also on the fold level (∼80%) (see Birzele et al., and ). Moreover, it is a very s […]

library_books

Alignment free local structural search by writhe decomposition

2010
Bioinformatics
PMCID: 2859133
PMID: 20371498
DOI: 10.1093/bioinformatics/btq127

[…] The SSE footprint vectors are computed by a downloadable program (Zotenko et al., ) and the vector comparison is carried out by an inhouse Perl implementation.SSEA (McGuffin et al., ): the filter for Vorolign (Birzele et al., ). SSEA treats a structure as a string of SSEs and aligns a pair of structures by the standard dynamic programming algorithm on this SSE string. As the raw alignment score ga […]

library_books

Flexible structural protein alignment by a sequence of local transformations

2009
Bioinformatics
PMCID: 2940242
PMID: 19417057
DOI: 10.1093/bioinformatics/btp296

[…] now standard alignments that need flexibility, as discussed by Yuzhen and Godzik ().We tested 10 methods including ours: ProtDeform, SSAP (Taylor and Orengo, ), Dali, FlexProt, Matras, TMalign, Rash, Vorolign (Birzele et al., ), PPM and Matt. The results for FlexProt were poor and were eliminated from the figures because they may be caused by simple problems reading the PDB numberings, and also it […]

Citations

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Vorolign institution(s)
Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Munich, Germany

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