ArticleProtein science : a publication of the Protein Society2015
Rapid search for tertiary fragments reveals protein sequence-structure relationships.
Article in Protein science : a publication of the Protein Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
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- Designability of α-Helical Protein Filaments.Sub-cellular biochemistry · 2026Review
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- De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts.Science (New York, N.Y.) · 2025Article
- De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties.Journal of the American Chemical Society · 2025Article
- Computationally designed stem-epitope mimetics elicit broadly reactive antibodies.bioRxiv : the preprint server for biology · 2025Article
- De novo design of four-helix bundle proteins to bind metalloporphyrin cofactors.Methods in enzymology · 2025Article
- Collagen-targeted protein nanomicelles for the imaging of non-alcoholic steatohepatitis.Acta biomaterialia · 2024Article
- Protocol for DesigningJournal of computational biology : a journal of computational molecular cell biology · 2024Article
5 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure-sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure.
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