ArticleProteins2021
Perturbing the energy landscape for improved packing during computational protein design.
Article in Proteins, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed.
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- Systems-Scale Structural Modeling Reveals the Germline Architecture of Immunodominance.bioRxiv : the preprint server for biology · 2026Article
- Intensity modulation of trichromatic split fluorescent proteins for live cell mapping.Cell reports methods · 2026Article
- Conformational equilibria in the activation of cystine-knot hormone receptors.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Using experimental results of protein design to guide biomolecular energy-function development.PLoS computational biology · 2026Article
- Small-molecule binding and sensing with a designed protein family.Nature communications · 2026Article
- Dynamic domain interactions encode possible CheA autophosphorylation mechanisms revealed by coarse-grained simulations.Biophysical journal · 2026Article
- ProteinDJ: A high-performance and modular protein design pipeline.Protein science : a publication of the Protein Society · 2026Article
- Dominant-negative TP53 mutations potentiated by the HSF1-regulated proteostasis network.Molecular cell · 2026Article
- Computational design of dynamic biosensors for emerging synthetic opioids.Nature communications · 2026Article
- Computational design of orthogonal TCR α/β interfaces for dual-TCR therapeutics.bioRxiv : the preprint server for biology · 2026Article
- Reinforced molecular dynamics: Physics-infused generative machine learning model simulates protein motion.PNAS nexus · 2026Article
- Computational design of 3C-like protease substrate peptide for modular detection of protease activity of coronavirus.Engineering in life sciences · 2026Article
- Dynamic domain interactions encode possible CheA autophosphorylation mechanisms revealed by coarse-grained simulations.bioRxiv : the preprint server for biology · 2025Article
- Manipulation of 7‑Finger Zinc Finger Nuclease Increases the Efficiency of Genome Editing in Human Cells.ACS bio & med chem Au · 2025Article
- High-resolution analysis of the human T-cell leukemia virus capsid protein reveals insights into immature particle morphology.Nature communications · 2025Article
- Article
- A protein dynamics-based deep learning model enhances predictions of fitness and epistasis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design.bioRxiv : the preprint server for biology · 2025Article
- Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints.Communications biology · 2025Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
The FastDesign protocol in the molecular modeling program Rosetta iterates between sequence optimization and structure refinement to stabilize de novo designed protein structures and complexes. FastDesign has been used previously to design novel protein folds and assemblies with important applications in research and medicine. To promote sampling of alternative conformations and sequences, FastDesign includes stages where the energy landscape is smoothened by reducing repulsive forces. Here, we discover that this process disfavors larger amino acids in the protein core because the protein compresses in the early stages of refinement. By testing alternative ramping strategies for the repulsive weight, we arrive at a scheme that produces lower energy designs with more native-like sequence composition in the protein core. We further validate the protocol by designing and experimentally characterizing over 4000 proteins and show that the new protocol produces higher stability proteins.
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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.