ArticleProteins2010
Extending the PRIME model for protein aggregation to all 20 amino acids.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed.
- In silico peptide self-assembly reveals the importance of N-terminal motifs and the inhibition mechanism of the mutation L38M in α-synuclein fibrillation.Protein science : a publication of the Protein Society · 2026Article
- Computational Study of the Dimerization of the Parathyroid Hormone.The journal of physical chemistry. B · 2025Article
- Design of parallel 𝛽-sheet nanofibrils using Monte Carlo search, coarse-grained simulations, and experimental testing.Protein science : a publication of the Protein Society · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Computational Design of Peptides for Biomaterials Applications.ACS applied bio materials · 2024Review
- Side-Chain Chemistry Governs Hierarchical Order of Charge-Complementary β-sheet Peptide Coassemblies.Angewandte Chemie (International ed. in English) · 2023Article
- Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations.PLoS computational biology · 2023Article
- Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering.Biomacromolecules · 2023Article
- Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations.Current opinion in chemical biology · 2023Review
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides.PNAS nexus · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- De novo design of peptides that coassemble into β sheet-based nanofibrils.Science advances · 2021Article
- Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic.Angewandte Chemie (International ed. in English) · 2021Review
- Structural Arrangement within a Peptide Fibril Derived from the Glaucoma-Associated Myocilin Olfactomedin Domain.The journal of physical chemistry. B · 2021Article
- Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics.AIChE journal. American Institute of Chemical Engineers · 2021Article
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations.Fluid phase equilibria · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
We extend PRIME, an intermediate-resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, to the description of the geometry and energetics of peptides containing all 20 amino acid residues. The 20 amino acid side chains are classified into 14 groups according to their hydrophobicity, polarity, size, charge, and potential for side chain hydrogen bonding. The parameters for extended PRIME, called PRIME 20, include hydrogen-bonding energies, side chain interaction range and energy, and excluded volume. The parameters are obtained by applying a perceptron-learning algorithm and a modified stochastic learning algorithm that optimizes the energy gap between 711 known native states from the PDB and decoy structures generated by gapless threading. The number of independent pair interaction parameters is chosen to be small enough to be physically meaningful yet large enough to give reasonably accurate results in discriminating decoys from native structures. The most physically meaningful results are obtained with 19 energy parameters.
Indexed as
Identifiers
What OpenQuestion holds
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.