ArticleMolecules (Basel, Switzerland)2020
Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering.
Article in Molecules (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Effects of ohmic heating-modified okara on the structural characteristics and quality properties of heat-induced myofibrillar protein gels.Food chemistry: X · 2026Article
- Interfacial Interactions between Nanoplastics and Biological Systems: toward an Atomic and Molecular Understanding of Plastics-Driven Biological Dyshomeostasis.ACS applied materials & interfaces · 2024Article
- Novel Insights into Understanding the Molecular Dialogues between Bipolaroxin and the Gα and Gβ Subunits of the Wheat Heterotrimeric G-Protein during Host-Pathogen Interaction.Antioxidants (Basel, Switzerland) · 2022Article
- Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody.Biomolecules · 2022Article
- Elucidation of the hetero-dimeric binding activity of LasR and RhlR proteins with the promoter DNA and the role of a specific Phe residue during the biosynthesis of HCN synthase from opportunistic pathogen Pseudomonas aeruginosa.Journal of molecular modeling · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
Controlling the quality of tertiary structures computed for a protein molecule remains a central challenge in de-novo protein structure prediction. The rule of thumb is to generate as many structures as can be afforded, effectively acknowledging that having more structures increases the likelihood that some will reside near the sought biologically-active structure. A major drawback with this approach is that computing a large number of structures imposes time and space costs. In this paper, we propose a novel clustering-based approach which we demonstrate to significantly reduce an ensemble of generated structures without sacrificing quality. Evaluations are related on both benchmark and CASP target proteins. Structure ensembles subjected to the proposed approach and the source code of the proposed approach are publicly-available at the links provided in Section 1.
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Registered trials
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