ArticleJournal of molecular biology2019
EvoDesign: Designing Protein-Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function.
Article in Journal of molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Advancing NanoLuc Luciferase Stability beyond Directed Evolution and Rational Design through Expert-Guided Deep Learning.ACS catalysis · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- Deep learning-guided rational engineering of synergistic PD-1 and LAG-3 blockade for enhanced tumor immunomodulation.Journal of computer-aided molecular design · 2025Article
- Evolution-guided design of mini-protein for high-contrastActa pharmaceutica Sinica. B · 2025Article
- A structural machine learning approach for rapid prediction of thermodynamically destabilizing tyrosine phosphorylations.Cell reports methods · 2025Article
- Influence of mutations at different distances from the active center on the activity and stability of laccase 13B22.Bioresources and bioprocessing · 2025Article
- Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS.Cell reports methods · 2025Article
- Decoding the effects of mutation on protein interactions using machine learning.Biophysics reviews · 2025Review
- Predicting Antibody Affinity Changes upon Mutation Based on Unbound Protein Structures.International journal of molecular sciences · 2025Article
- Computational analysis reveals temperature-induced stabilization of FAST-PETase.Computational and structural biotechnology journal · 2025Article
- Rapid prediction of thermodynamically destabilizing tyrosine phosphorylations in cancers.bioRxiv : the preprint server for biology · 2024Article
- Article
- LoCoHD: a metric for comparing local environments of proteins.Nature communications · 2024Article
- Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.International journal of molecular sciences · 2024Review
- What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.Journal of molecular biology · 2023Article
- Decoding CRISPR-Cas PAM recognition with UniDesign.Briefings in bioinformatics · 2023Article
- Computational Protein Design for COVID-19 Research and Emerging Therapeutics.ACS central science · 2023Review
- De novo protein fold design through sequence-independent fragment assembly simulations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- PROT-ON: A structure-based detection of designer PROTein interface MutatiONs.Frontiers in molecular biosciences · 2023Article
- Article
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Authors and funding
4 authors.
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Abstract
EvoDesign (https://zhanglab.ccmb.med.umich.edu/EvoDesign) is an online server system for protein design. The method uses evolutionary profiles to guide the sequence search simulation and demonstrated significant advantages over physics-based approaches in terms of more accurately designing proteins that adopt desired target folds. Despite the success, the previous EvoDesign program focused only on monomer protein design, which limited its ability and usefulness in terms of designing functional proteins. In this work, we propose a new EvoDesign server, which extends the principles of evolution-based design to design protein-protein interactions. Starting from a two-chain complex structure, structurally similar interfaces are identified from known protein-protein interaction databases. An interface evolutionary profile is then constructed from a multiple sequence alignment of the interface analogies, which is combined with a newly developed, atomic-level physical energy function to guide the replica-exchange Monte Carlo simulation search. The purpose of the server is to redesign the specified complex chain to increase its stability and binding affinity for the other chain in the complex. With the improved scope and accuracy of the methodology, the new EvoDesign pipeline should become a useful online tool for functional protein design and drug discovery studies.
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Registered trials
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