ArticleBioinformatics (Oxford, England)2016
Protein backbone ensemble generation explores the local structural space of unseen natural homologs.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 9 citations in OpenAlex.
- Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape.Sensors (Basel, Switzerland) · 2024Article
- Protein structure generation via folding diffusion.Nature communications · 2024Article
- Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders.Brain : a journal of neurology · 2023Article
- Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation.The journal of physical chemistry. B · 2018Article
- Pushing the Backbone in Protein-Protein Docking.Structure (London, England : 1993) · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
motivationMutations in homologous proteins affect changes in the backbone conformation that involve a complex interplay of forces which are difficult to predict. Protein design algorithms need to anticipate these backbone changes in order to accurately calculate the energy of the structure given an amino acid sequence, without knowledge of the final, designed sequence. This is related to the problem of predicting small changes in the backbone between highly similar sequences.
resultsWe explored the ability of the Rosetta suite of protein design tools to move the backbone from its position in one structure (template) to its position in a close homologous structure (target) as a function of the diversity of a backbone ensemble constructed using the template structure, the percent sequence identity between the template and target, and the size of local zone being considered in the ensemble. We describe a pareto front in the likelihood of moving the backbone toward the target as a function of ensemble diversity and zone size. The equations and protocols presented here will be useful for protein design. AVAILABILITY AND IMPLEMENTATION: PyRosetta scripts available at www.bioinfo.rpi.edu/bystrc/downloads.html#ensemble CONTACT: bystrc@rpi.edu.
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