ArticleMethods in molecular biology (Clifton, N.J.)2017
An Evolution-Based Approach to De Novo Protein Design.
Article in Methods in molecular biology (Clifton, N.J.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Computational design of class II MHC binding peptide with sequence-based evolution information.Bioinformatics advances · 2026Article
- Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution.Viruses · 2021Article
- Multiobjective heuristic algorithm forComputational and structural biotechnology journal · 2021Article
- Article
- Multi-state design of flexible proteins predicts sequences optimal for conformational change.PLoS computational biology · 2020Article
- A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target. The observed frequencies of amino acids in specific positions in the structure in the form of structural profiles collected from proteins with similar folds and complexes with similar interfaces can implicitly capture many subtle effects that are essential for correct folding and protein-binding interactions. As a result of the inclusion of evolutionary information, the sequences designed by EvoDesign have native-like folding and binding properties not seen by other physics-based design methods. In this chapter, we describe how EvoDesign can be used to redesign proteins with a focus on the computational and experimental procedures that can be used to validate the designs.
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