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Other literature type . 2026
License: CC BY
Data sources: Datacite
ZENODO
Other literature type . 2026
License: CC BY
Data sources: Datacite
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Infinite Synthesis: Amortized O(1) Protein Folding via 6DoF Manifold Projection

Authors: Lynch, Brendan;

Infinite Synthesis: Amortized O(1) Protein Folding via 6DoF Manifold Projection

Abstract

Conventional protein folding methods rely on computationally intensive molecular dynamics or iterative optimization heuristics. This work introduces the Chimera framework, which employs a fast 6-degree-of-freedom (6DoF) geometric resolver to map the manifold of physically allowed backbone rotations. A specialized Transformer is trained on high-fidelity “Geometric Truth” extracted from 37 high-resolution PDB structures. The resulting model solves protein structures including unknown segments (“Z-gaps”) in amortized constant time (≈2 ms per protein on consumer Apple Silicon hardware) with sub-ångström backbone precision (motive MSE ≈ 0.0197 on benchmark structures). We demonstrate high throughput (∼43 million proteins/day), effective de-novo bridge sequence design via geometric smoothness and clash scoring, and strong generalization on synthetic chimeric sequences. The approach reframes folding as deterministic manifold projection rather than search, offering a scalable path toward real-time structural biology and therapeutic protein design. Source code and the trained UFT-Global-Brain-V2 weights are provided to ensure full reproducibility of the $O(1)$ benchmark.

Keywords

spectral regularization, Base-24 quantization, de-novo bridge design, computational biology, Z-gap resolution, sub-ångström precision, protein folding, 6DoF manifold, amortized O(1), structural biology, backbone prediction, Transformer geometry, Chimera training

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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