ReviewProtein science : a publication of the Protein Society2012
Multistate approaches in computational protein design.
Review in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed.
- Multistate Enzyme Design Enables Efficient and Stereoselective Multistep Catalysis.bioRxiv : the preprint server for biology · 2026Article
- Dynamic-Structure Redesign of Calmodulin Reveals Mechanistic Constraints on Ryr2 Regulation.bioRxiv : the preprint server for biology · 2026Article
- AI-Driven De Novo Binder Design: From Structure Prediction to Closed-Loop Optimization.Computational and structural biotechnology journal · 2026Review
- Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico.Human vaccines & immunotherapeutics · 2025Review
- Designing Enzymatic Reactivity with an Expanded Palette.Chembiochem : a European journal of chemical biology · 2025Review
- Deep learning-guided design of dynamic proteins.Science (New York, N.Y.) · 2025Article
- A de novo designed coiled coil-based switch regulates the microtubule motor kinesin-1.Nature chemical biology · 2024Article
- A general computational design strategy for stabilizing viral class I fusion proteins.Nature communications · 2024Article
- Review
- Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Computational remodeling of an enzyme conformational landscape for altered substrate selectivity.Nature communications · 2023Article
- Disentangling contact and ensemble epistasis in a riboswitch.Biophysical journal · 2023Article
- The road to fully programmable protein catalysis.Nature · 2022Review
- Computational Design of Miniprotein Binders.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Step-by-step design of proteins for small molecule interaction: A review on recent milestones.Protein science : a publication of the Protein Society · 2021Review
- Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms.FEMS microbiology reviews · 2021Review
- Structural resolution of switchable states of a de novo peptide assembly.Nature communications · 2021Article
- Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network.PloS one · 2021Article
- Harnessing Conformational Plasticity to Generate Designer Enzymes.Journal of the American Chemical Society · 2020Review
- Toward fine-tuned metabolic networks in industrial microorganisms.Synthetic and systems biotechnology · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational protein design (CPD) is a useful tool for protein engineers. It has been successfully applied towards the creation of proteins with increased thermostability, improved binding affinity, novel enzymatic activity, and altered ligand specificity. Traditionally, CPD calculations search and rank sequences using a single fixed protein backbone template in an approach referred to as single-state design (SSD). While SSD has enjoyed considerable success, certain design objectives require the explicit consideration of multiple conformational and/or chemical states. Cases where a "multistate" approach may be advantageous over the SSD approach include designing conformational changes into proteins, using native ensembles to mimic backbone flexibility, and designing ligand or oligomeric association specificities. These design objectives can be efficiently tackled using multistate design (MSD), an emerging methodology in CPD that considers any number of protein conformational or chemical states as inputs instead of a single protein backbone template, as in SSD. In this review article, recent examples of the successful design of a desired property into proteins using MSD are described. These studies employing MSD are divided into two categories--those that utilized multiple conformational states, and those that utilized multiple chemical states. In addition, the scoring of competing states during negative design is discussed as a current challenge for MSD.
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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.