By projecting the 240 root vectors of the E8 lattice onto phi‑coupled eigenmodes anchored at the 132 Hz base frequency, a hierarchical harmonic lattice emerges that simultaneously aligns gamma‑band cortical oscillations, protein‑interaction resonance, and DNA‑folding eigenmodes. This lattice functions as a topologicall...
Andrew Stewart Caldin· Zenodo (CERN European Organi...· 0 citations
Protein Fold: How It Works The Ly‑Algebra Pipeline – From Sequence to Pentamer Welcome to the Protein Fold platform. This document walks you through the computational pipeline that takes a single amino acid sequence and produces a refined monomer and a 5‑fold symmetric pentameric assembly, all powered by the Ly‑Algebra...
Chloe Tully· Zenodo (CERN European Organi...· 0 citations
By extending the SYK holographic wormhole simulation, we map the 240 E8 root vectors onto a protein‑folding scaffold that acts as a quantum‑biological interface. A 132 Hz nanomechanical resonator array, phi‑scaled to the E8 lattice, drives distinct harmonic modes that imprint each root vector onto a specific protein co...
Andrew Stewart Caldin· Zenodo (CERN European Organi...· 0 citations
By mapping the 240 E8 root vectors onto the hierarchical folding of protein-folding landscapes, we establish a reciprocal feedback loop between quantum information and macro-biological states. The $\phi$-modulated phase alignment creates a bridge where neural firing patterns are treated as discrete intersections of the...
Andrew Stewart Caldin· Zenodo (CERN European Organi...· 0 citations
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The DNA damage response preserves genome integrity by detecting DNA lesions, activating checkpoint signalling, and coordinating repair with cell-cycle control. Defective or incomplete repair can promote mutation accumulation, chromosomal instability, cancer development, and ageing-associated diseases. In this review,...
Armin Sharifi, Amila Suraweera, K. J. O'Byrne et al.· Cellular Oncology· 0 citations
Supporting material for the manuscript The Geometry of Allostery: Quantifying Pathway Organization in Protein Networks (Fatma Şengüler Çiftçi and Burak Erman, Koç University). The paper works out what happens when you take Laplacian minors of a protein contact network past the pairwise level. The first minor counts spa...
Results show that current co-folding methods remain unreliable as stand-alone predictors of ion-channel ligand-binding modes and highlight pose sampling, pocket selection, ligand representation and independent structural validation as priorities for methodological development.
Yu Zhu, Taufiq Rahman· Frontiers in Biophysics· 0 citations
Supporting material for the manuscript The Geometry of Allostery: Quantifying Pathway Organization in Protein Networks (Fatma Şengüler Çiftçi and Burak Erman, Koç University). The paper works out what happens when you take Laplacian minors of a protein contact network past the pairwise level. The first minor counts spa...
Background: Non-alcoholic fatty liver disease (NAFLD) is currently the most common chronic liver disorder and is closely linked to insulin resistance and the metabolic syndrome. Beyond the accumulation of triacylglycerides (TAG), disturbed hepatic cholesterol handling — mediated by the low-density lipoprotein receptor...
Jahongir Kh. Tursunov, Ulugbek Z. Zaribbaev, A. Abduvaliev et al.· International journal of med...· 0 citations
Intrinsically disordered regions (IDRs) mediate protein interactions through poorly understood mechanisms. We studied the retinoblastoma protein (pRb) and its interaction with the SV40 Large T antigen (LTSV40), a viral oncoprotein that displaces E2F factors. Using molecular dynamics and umbrella sampling, we show the L...
Carla Luciana Padilla Franzotti, Nicolás Palópoli, Gustavo Pierdominici‐Sottile et al.· Zenodo (CERN European Organi...· 0 citations
Intrinsically disordered regions (IDRs) mediate protein interactions through poorly understood mechanisms. We studied the retinoblastoma protein (pRb) and its interaction with the SV40 Large T antigen (LTSV40), a viral oncoprotein that displaces E2F factors. Using molecular dynamics and umbrella sampling, we show the L...
Carla Luciana Padilla Franzotti, Nicolás Palópoli, Gustavo Pierdominici‐Sottile et al.· Zenodo (CERN European Organi...· 0 citations
CIR-DDG, a lightweight residual adapter that combines a fixed base prediction with 22 interpretable descriptors of cross-chain distance, contact density and site--partner context, is introduced, showing that the learned geometric correction generalizes beyond SKEMPI thermodynamic measurements.
Weizhen Yu, Zhi-Heng Zou, Yong-Gui Huang et al.· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
