protein folding

Quantum Biology-Inspired Bioinformatics Algorithms

This paper explores the application of principles from quantum biology to design novel bioinformatics algorithms. Traditional bioinformatics relies heavily on classical computational models, often neglecting the potential influence of quantum effects observed within biological systems. This research proposes a framewor...

Locus-resolved reconstruction of the pig UGT family reveals an isoform-collapse artifact in frozen ESM-2 retrieval

Deep mutational scanning of CYP2C9, CYP2C19, and NUDT15 shows that pharmacogene variant interpretation requires assay-specific functional data.

This dimensionality dominates the data, and a supervised ESM-2 sequence baseline was benchmarked against the ESM1v zero-shot ensemble and AlphaMissense under position-based 5-fold cross-validation, together with three architectural extensions: AlphaFold structural features, multi-task learning across paired assays, and...

Biological Molecular Protein Folding: A Dynamic Modeling Approach

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...

Title: Non-Standard Geometry – Computational Geometry of Complex Systems

This paper explores the application of non-standard geometry to computational geometry, focusing on the development of a novel method for defining and computing geometric properties for complex systems, particularly fluid dynamics and protein folding. Traditional geometric computation often struggles with the inherent...

Quantum Biology-Inspired Bioinformatics Algorithms

This paper explores the application of principles from quantum biology to design novel bioinformatics algorithms. Traditional bioinformatics relies heavily on classical computational models, often neglecting the potential influence of quantum effects observed within biological systems. This research proposes a framewor...

Deterministic Topological Neutralization of the Aβ42 N-Terminal Stacking Interface by a D-Enantiomer RDK Cap

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-...

People behind the ideas

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...

Graph Neural Networks for Protein Structure Prediction

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...

Title: Non-Standard Geometry – Computational Geometry of Complex Systems

This paper explores the application of non-standard geometry to computational geometry, focusing on the development of a novel method for defining and computing geometric properties for complex systems, particularly fluid dynamics and protein folding. Traditional geometric computation often struggles with the inherent...

Graph Neural Networks for Predicting Protein Folding Pathways

Predicting the folding pathway of a protein – the process by which a linear chain of amino acids adopts its functional three-dimensional structure – is a central challenge in computational biology. Existing methods often struggle to accurately represent the intricate and dynamic interactions between amino acids that go...

Biological Molecular Protein Folding: A Dynamic Modeling Approach

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...