ArticleNucleic acids research2013
EvoDesign: De novo protein design based on structural and evolutionary profiles.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Review
- Advancing NanoLuc Luciferase Stability beyond Directed Evolution and Rational Design through Expert-Guided Deep Learning.ACS catalysis · 2026Article
- Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.Applied biochemistry and biotechnology · 2025Review
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- The Damietta Server: a comprehensive protein design toolkit.Nucleic acids research · 2024Article
- Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review.Molecules (Basel, Switzerland) · 2023Review
- Article
- 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
- EvoDesign: Designing Protein-Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function.Journal of molecular biology · 2019Article
- DAMpred: Recognizing Disease-Associated nsSNPs through Bayes-Guided Neural-Network Model Built on Low-Resolution Structure Prediction of Proteins and Protein-Protein Interactions.Journal of molecular biology · 2019Article
- Changing the Apoptosis Pathway through Evolutionary Protein Design.Journal of molecular biology · 2019Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- Computational approaches forBioscience reports · 2017Review
- An Evolution-Based Approach to De Novo Protein Design.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Evaluating the accuracy of protein design using native secondary sub-structures.BMC bioinformatics · 2016Article
- UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.Nucleic acids research · 2016Article
- Preface.Methods in enzymology · 2016Article
- Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles.PLoS computational biology · 2015Article
- Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering.Journal of structural biology · 2015Article
- Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure.European journal of inorganic chemistry · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
Protein design aims to identify new protein sequences of desirable structure and biological function. Most current de novo protein design methods rely on physics-based force fields to search for low free-energy states following Anfinsen's thermodynamic hypothesis. A major obstacle of such approaches is the inaccuracy of the force field design, which cannot accurately describe the atomic interactions or distinguish correct folds. We developed a new web server, EvoDesign, to design optimal protein sequences of given scaffolds along with multiple sequence and structure-based features to assess the foldability and goodness of the designs. EvoDesign uses an evolution-profile-based Monte Carlo search with the profiles constructed from homologous structure families in the Protein Data Bank. A set of local structure features, including secondary structure, torsion angle and solvation, are predicted by single-sequence neural-network training and used to smooth the sequence motif and accommodate the physicochemical packing. The EvoDesign algorithm has been extensively tested in large-scale protein design experiments, which demonstrate enhanced foldability and structural stability of designed sequences compared with the physics-based designing methods. The EvoDesign server is freely available at http://zhanglab.ccmb.med.umich.edu/EvoDesign.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.