ArticleSource code for biology and medicine2007
Pspace: a program that assesses protein space.
Article in Source code for biology and medicine, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Subsequence Propensities.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundWe describe a computer program named Pspace designed to a) obtain a reliable basis for the description of three-dimensional structures of a given protein family using homology modeling through selection of an optimal subset of the protein family whose structure would be determined experimentally; and b) aid in the search of orthologs by matching two sets of sequences in three different ways.
methodsThe prioritization is established dynamically as new sequences and new structures are becoming available through ranking proteins by their value in providing structural information about the rest of the family set. The matching can give a list of potential orthologs or it can deduce an overall optimal matching of two sets of sequences.
resultsThe various covering strategies and ortholog searches are tested on the bromodomain family.
conclusionThe possibility of extending this approach to the space of all proteins is discussed.
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Registered trials
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