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2,047 papers
Protein folding is a fundamental process in biology, crucial for protein function and stability. Traditional methods often rely on rigid, predefined folding rules, limiting flexibility and efficiency. This paper introduces a novel computational approach – a dynamic modeling algorithm – that adapts protein structure dur...
All information has an origin story and it is not the person, it is the data. This is my origin story for my project. These are from files a year and some change ago. When I started to gather the pieces together of my year and a half of researching. It is nice that everyone appreciates a final product because that mean...
================================================================================EXECUTIVE SUMMARY: THE DEATH OF THE BLACK BOX================================================================================The modern AI industry is built on a statistical hallucination: trillion-parameter models consuming megawatts of en...
This paper presents a novel approach to protein structure prediction leveraging the principles of quantum entanglement. Traditional protein structure prediction methods are often limited by the computational complexity of simulating large biomolecular systems. We propose a framework that utilizes quantum entanglement t...
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Deterministic Topological Neutralization of the Aβ42 N-Terminal Stacking Interface by a D-Enantiomer RDK Cap This repository contains a theoretical computational proof of topological interface neutralization on a custom-physics protein-fold ledger. By utilizing a deterministic, non-Cartesian discrete topology (Axiom I-...
Resonance-Based Probability Distribution Modeling presents a novel probabilistic modeling framework predicated on the principles of resonant frequencies and vibrational modes within complex systems. This approach aims to enhance predictive accuracy across diverse domains, including protein folding, fluid dynamics, and...
Abstract Background During host colonization, fungal plant pathogens secrete effector-like proteins that alter host cell physiology and target plant-associated microbes. However, rapid evolution and low sequence conservation hinder the study and characterization of these proteins. The fungus Zymoseptoria passerinii inf...
Protein folding is the chemistry of the sequence's decision: how a chain of amino acids—with astronomically many possible conformations—finds its native state in milliseconds, the paradox Cyrus Levinthal posed in 1968 and Christian Anfinsen's thermodynamic hypothesis answered: the sequence itself encodes the fold. This...
Protein folding is the chemistry of the sequence's decision: how a chain of amino acids—with astronomically many possible conformations—finds its native state in milliseconds, the paradox Cyrus Levinthal posed in 1968 and Christian Anfinsen's thermodynamic hypothesis answered: the sequence itself encodes the fold. This...
Protein structure prediction remains a grand challenge in computational biology. Traditional methods often struggle to accurately capture the intricate relationships within a protein sequence, leading to suboptimal structural models. This work explores the application of Graph Neural Networks (GNNs) to address this cha...
dFTN ferritin domains are described, which expand the range of known ferritin family proteins and provide insight into Asgard archaea iron metabolism.
It is proposed that HP6/Umbrea acts like a plasticizer, a molecular softener that could make otherwise silenced heterochromatic genes leakier and thus potentially act as a rheostat for leaky transcription.
Proof of concept for watermarking AI-generated proteins while preserving biological function.
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.
Scientists are using AlphaFold to strengthen a photosynthesis enzyme for resilient, heat-tolerant crops.
Explore how AlphaFold has accelerated science and fueled a global wave of biological discovery.
AlphaFold has revealed the structure of a key protein behind heart disease
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