ArticleProteins2020
High-accuracy protein structures by combining machine-learning with physics-based refinement.
Article in Proteins, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering.Frontiers in immunology · 2021Pooled it
- Computational optimization of DEK1 calpain domain solubility through integrated structural modelling and data-driven targeted mutagenesis.Scientific reports · 2026Article
- The transformative impact of AI-enabled AlphaFold 3: evolution, current status, and future prospects in structural biology.Frontiers in artificial intelligence · 2026Review
- Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and AmideInternational journal of molecular sciences · 2025Article
- A molecular dynamics study of membrane positioning for 7-transmembrane RGS proteins to modulate G-protein-mediated signaling in plants.Computational and structural biotechnology journal · 2025Article
- Identification and Optimization of more Efficient Olivetolic Acid Synthases.Cannabis and cannabinoid research · 2024Article
- Downregulation of PIK3IP1/TrIP on T cells is controlled by TCR signal strength, PKC and metalloprotease-mediated cleavage.bioRxiv : the preprint server for biology · 2024Article
- AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants.Biology · 2024Article
- The origin and structural evolution of de novo genes in Drosophila.Nature communications · 2024Article
- Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction.Journal of chemical information and modeling · 2024Article
- HLA-EpiCheck: novel approach for HLA B-cell epitope prediction using 3D-surface patch descriptors derived from molecular dynamic simulations.Bioinformatics advances · 2024Article
- CD44 connects autophagy decline and ageing in the vascular endothelium.Nature communications · 2023Article
- iQDeep: an integrated web server for protein scoring using multiscale deep learning models.Journal of molecular biology · 2023Article
- Molecular basis for protein histidine N1-specific methylation of the "His-x-His" motifs by METTL9.Cell insight · 2023Article
- Using AlphaFold Predictions in Viral Research.Current issues in molecular biology · 2023Review
- Development of a charged model of the SARS-CoV-2 viral surface.Biochimica et biophysica acta. Biomembranes · 2023Article
- Novel machine learning approaches revolutionize protein knowledge.Trends in biochemical sciences · 2023Review
- Designing Collagen-Binding Peptide with Enhanced Properties Using Hydropathic Free Energy Predictions.Applied sciences (Basel, Switzerland) · 2023Article
- Scalable Inhibitors of the Nsp3-Nsp4 Coupling in SARS-CoV-2.ACS omega · 2023Article
- Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Protein structure prediction has long been available as an alternative to experimental structure determination, especially via homology modeling based on templates from related sequences. Recently, models based on distance restraints from coevolutionary analysis via machine learning to have significantly expanded the ability to predict structures for sequences without templates. One such method, AlphaFold, also performs well on sequences where templates are available but without using such information directly. Here we show that combining machine-learning based models from AlphaFold with state-of-the-art physics-based refinement via molecular dynamics simulations further improves predictions to outperform any other prediction method tested during the latest round of CASP. The resulting models have highly accurate global and local structures, including high accuracy at functionally important interface residues, and they are highly suitable as initial models for crystal structure determination via molecular replacement.
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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.