ReviewProtein engineering, design & selection : PEDS2022
The stability and dynamics of computationally designed proteins.
Review in Protein engineering, design & selection : PEDS, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Article
- Silk-based microparticles for the adsorption of methylene blue: formulations, characterization, adsorption study,RSC advances · 2025Article
- Network pharmacology, molecular docking, molecular dynamics simulation, and experiment verification analysis to reveal the action mechanism of RenShen Guipi Wan in the treatment of anemia.Biotechnology letters · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- EquilibraTor streamlines molecular dynamics simulations in a single execution.Computational and structural biotechnology journal · 2025Article
- Enhancement of the Thermostability ofMolecules (Basel, Switzerland) · 2024Article
- Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis.Journal of biological engineering · 2024Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic NaInternational journal of molecular sciences · 2024Article
- NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN.International journal of molecular sciences · 2024Article
- Article
- The Potential Mechanism of Liujunzi Decoction in the Treatment of Breast Cancer based on Network Pharmacology and Molecular Docking Technology.Current pharmaceutical design · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Protein stability, dynamics and function are intricately linked. Accordingly, protein designers leverage dynamics in their designs and gain insight to their successes and failures by analyzing their proteins' dynamics. Molecular dynamics (MD) simulations are a powerful computational tool for quantifying both local and global protein dynamics. This review highlights studies where MD simulations were applied to characterize the stability and dynamics of designed proteins and where dynamics were incorporated into computational protein design. First, we discuss the structural basis underlying the extreme stability and thermostability frequently observed in computationally designed proteins. Next, we discuss examples of designed proteins, where dynamics were not explicitly accounted for in the design process, whose coordinated motions or active site dynamics, as observed by MD simulation, enhanced or detracted from their function. Many protein functions depend on sizeable or subtle conformational changes, so we finally discuss the computational design of proteins to perform a specific function that requires consideration of motion by multi-state design.
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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.