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114 results for “protein folding mechanisms”

Closest match to your words first, in the title, the authors, the abstract or Pith's review. Among equal matches, newer papers first. The order is not a quality score.

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  1. The paper:

    Inferring protein folding mechanisms from natural sequence diversity

    Biology · arXiv:2412.14341

    Ezequiel A. Galpern, Ernesto A. Roman, Diego U. Ferreiro

    Pith says

    Machine review · deepseek-v4-flash · 11 Aug 2026 · what was read was not recorded

    Holds up, with conditions. A well-controlled extension of the foldon Ising model to globular proteins, with real validation and honest caveats; the folding-dominance assumption is the main soft spot, but the paper deserves a serious referee.

    4 major objections, the first at Introduction; Eq. (2); Fig. S12; Table S2; Concluding … · 5 minor

  2. From the paper: …To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein …

  3. From the paper: …and Parisi to describe some of the features of protein folding mechanisms. We study how the (folded) shape of the chain evolves in time. We find that for …

  4. The paper:

    Two Stages of Folding: Convergent Mechanisms in AI Protein Folding Trunks

    Computer Science · arXiv:2602.06020

    Kevin Lu, Jannik Brinkmann, Stefan Huber and 4 more

    Pith says

    Machine review · deepseek-v4-flash · 3 Aug 2026 · what was read was not recorded

    Holds up, with conditions. The ESMFold two-stage story is real and well-supported; the abstract's three-model convergence claim is not in the body and should be rewritten before publication.

    3 major objections, the first at Abstract; §1; §7; App. A · 4 minor

  6. The paper:

    Predicting protein folding dynamics using sequence information

    Biology · arXiv:2505.17237

    Ezequiel A. Galpern, Federico Caamaño, Diego U. Ferreiro

    Pith says

    Machine review · deepseek-v4-flash · 7 Aug 2026 · what was read was not recorded

    Holds up, with conditions. A clean, useful protocol that generalizes the authors' earlier Potts-plus-Ising work, but the 'sequence alone' claim is not validated by new experiments in this paper.

    5 major objections, the first at Methods, Step 2 (and Abstract/Box 1) · 5 minor

    From the paper: Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in …

  7. The paper:

    Enhancing Reinforcement learning in 3-Dimensional Hydrophobic-Polar Protein Folding Model with Attention-based layers

    Computer Science · arXiv:2504.15634

    Peizheng Liu, Hitoshi Iba

    Pith says

    Machine review · deepseek-v4-flash · 16 Aug 2026 · what was read was not recorded

    Holds up, with conditions. First attention-based DQN for 3D HP folding matches known best energies on four short benchmarks, but an internal inconsistency in the reported best-known values for Sequence 6 undermines the 'near-optimal' claim for longer chains.

    3 major objections, the first at Section 3.1, Tables 1 and 3 · 5 minor

    From the paper: …to the hydrophobic-hydrophilic (H-P) model for protein folding remains relatively unexplored. In this work, we adapt a Deep Q-Network (DQN) integrated with …

  8. From the paper: Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old …

  9. From the paper: Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a …

  10. From the paper: …three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is …

  11. From the paper: The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from …

  12. From the paper: Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a …

  13. From the paper: …optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the …

  14. From the paper: Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. …

  15. From the paper: Protein folding is a problem of large interest since it concerns the mechanism by which the genetic …

  16. From the paper: …in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding …

  17. From the paper: …nderstand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native …

  18. The paper:

    Understanding Reaction Mechanisms from Start to Finish

    Physics · arXiv:2507.04052

    Rik S. Breebaart, Gianmarco Lazzeri, Roberto Covino and 1 more

    Pith says

    Machine review · grok-4.3 · 19 May 2026 · what was read was not recorded

    Holds up, with conditions. The iterative TIS-plus-NN loop addresses the sampling-coordinate circularity in a practical way, but the accuracy claims rest on limited checks without error bars or exact references.

    3 major objections, the first at iteration loop and convergence criterion · 2 minor

  19. From the paper: …olate excipient mechanisms on hydrophobic interactions, relevant to both protein folding and biomolecular self-assembly. We …

  20. From the paper: Folding of proteins into their correct native structure is key to their function. Simultaneously, the …