Vorolign statistics

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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 in pipeline

2013
PMCID: 3578447
PMID: 23440025
DOI: 10.3389/fmicb.2012.00419

[…] 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 […]


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Vorolign in publications

 (7)
PMCID: 5753887
PMID: 29317803
DOI: 10.1177/1177932217747277

[…] (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 […]

PMCID: 3578447
PMID: 23440025
DOI: 10.3389/fmicb.2012.00419

[…] 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 […]

PMCID: 2935407
PMID: 20823310
DOI: 10.1093/bioinformatics/btq369

[…] with the alignment score. vorescore, a template-based protein structure model rescoring system is introduced. the method scores the model structure against the template used for the modeling using vorolign. the method works on models from different alignment methods and incorporates both knowledge from the prediction method and the rescoring., results: the performance of vorescore is evaluated […]

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

[…] practical structural search programs typically use sse matching programs as filters before engaging full alignment. for example, dalilite (holm and park, ) employs 3d-lookup (holm and sander, ) and vorolign (birzele et al., ) employs sse alignment algorithm (ssea, mcguffin et al., ) as fast filters. projection methods are typically even faster than these sse-based methods and thus […]

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

[…] that increases the number of compatible pairs on partial pair lists until an optimal pair list is reached under certain criteria for the allowed bending. the method outperforms tm-align and vorolign (birzele et al., ), this latter one, a method from the same research group., in general, the use of a single rigid transformation for protein comparison has gained much popularity among […]


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

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