Rapid efficient macromolecular substructure searching in a cloud

Voorst, Jeffrey R. Van; Finzel, Barry C.

doi:10.1145/2382936.2383017

Cited by 1 publication

(2 citation statements)

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“…A more detailed algorithm performance assessment and dependence on physical memory and parallelization has been presented elsewhere. 49 These results clearly show that the algorithm performs efficiently to identify similarly oriented helices irrespective of protein molecule of origin. Matches identified in separate cohorts (AA vs AB) retain similar characteristics, even in the amphipathic sequence preference for leucine in the helix pair interior, whether the matches originate in one molecule, or from the interaction of two.…”

Section: ■ Results and Discussionmentioning

confidence: 72%

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Searching for Likeness in a Database of Macromolecular Complexes

Voorst

Finzel

2013

J. Chem. Inf. Model.

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A software tool and workflow based on distance geometry is presented that can be used to search for local similarity in substructures in a comprehensive database of experimentally derived macromolecular structure. The method does not rely on fold annotation, specific secondary structure assignments, or sequence homology and may be used to locate compound substructures of multiple segments spanning different macromolecules that share a queried backbone geometry. This generalized substructure searching capability is intended to allow users to play an active part in exploring the role specific substructures play in larger protein domains, quaternary assemblies of proteins, and macromolecular complexes of proteins and polynucleotides. The user may select any portion or portions of an existing structure or complex to serve as a template for searching, and other structures that share the same structural features are identified, retrieved and overlaid to emphasize substructural likeness. Matching structures may be compared using a variety of integrated tools including molecular graphics for structure visualization and matching substructure sequence logos. A number of examples are provided that illustrate how generalized substructure searching may be used to understand both the similarity, and individuality of specific macromolecular structures. Web-based access to our substructure searching services is freely available at https://drugsite.msi.umn.edu.

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Section: ■ Results and Discussionmentioning

confidence: 72%

“…Also shown, is the sequence logo representing the ensemble of nonredundant matches. A more detailed algorithm performance assessment and dependence on physical memory and parallelization has been presented elsewhere …”

Section: Resultsmentioning

confidence: 99%