FiberForge: enabling high-throughput simulations of the mechanical properties of helical fibrils

2026/01/01 by Kieran Nehil-Puleo, Zhongyue Yang · 1 voice
Materials Science · Biochemistry, Genetics and Molecular Biology · #Supramolecular Self-Assembly in Materials #Calcium Carbonate Crystallization and Inhibition #Connective tissue disorders research

paper · pdf · doi:10.1039/d5dd00307e

openalex publication_date 2026/01/01 · openalex created_date 2026/02/03 · openalex updated_date 2026/05/21

Abstract

FiberForge provides an end-to-end platform for molecular modeling and design of amyloid materials, enabling physics-based identification of sequences and polymorphs with targeted mechanical behavior.

Citations

• A simple method for displaying the hydropathic character of a protein
• SciPy 1.0: fundamental algorithms for scientific computing in Python
• De novo design of protein structure and function with RFdiffusion
• PACKMOL: A package for building initial configurations for molecular dynamics simulations

Discussions

• 📢 Zhongyue (John) Yang introduces FiberForge: an open source workflow that automates molecular modelling, design and characterisation of amyloid fibrils in new #DigitalDiscovery manuscript! 🖥️ Read [bsky, 1 points, 0 comments]

Related

• Mechanical stretching of amyloid Abeta11-42 fibrils using steered molecular dynamics
• Functional Amyloid Fibrils as Versatile Tools for Novel Biomaterials
• Structural and thermodynamic classification of amyloid polymorphs
• Molecular Architecture and Helicity of Bacterial Amyloid Nanofibers: Implications for the Design of Nanoscale Antibiotics
• Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy