DiPhyx Stories
Modeling an RNA–Ligand Complex with Boltz-1
RNA aptamers are short nucleic acid sequences capable of binding to specific molecular targets with high affinity and selectivity. Among the most extensively studied of these is the theophylline aptamer—a 33-nucleotide RNA sequence that exhibits extraordinary specificity for the small molecule theophylline, distinguishing it from caffeine with over 10,000-fold selectivity, despite their near-identical structures. This makes the theophylline aptamer a compelling model for RNA-based recognition, biosensing, and molecular switch design.
Boltz-1
Boltz-1 is a state-of-the-art open-source model for predicting biomolecular structures, including combinations of proteins, RNA, DNA, covalent ligands, and glycans. It supports modified residues and allows conditioning on specific interaction pockets or contacts. Released under the MIT license, Boltz-1 is free for academic and commercial use.
JupyterLab vs. Notebook: Key Differences & Guide
Choosing the Right Tool for Your Data Science and Research Workflows
Volume Rendering in ParaView - DiPhyx Scientific Computing
The fundamentals of volume rendering in ParaView, practical steps and tips to help you effectively visualize your volumetric datasets.
Data Probing in ParaView
How to effectively use ParaView's data probing tools to extract and analyze specific data points, lines, and surfaces within datasets
Open Source VS Proprietary CFD Software
A concise comparison of open-source versus proprietary CFD software, highlighting key advantages, disadvantages, and examples.
The Evolution of Cloud CFD and Its Benefits
Learn about the advantages of cloud-based CFD and how platforms like DiPhyx are making it easier to adopt this powerful tool.
NGS Workflow Solution
Streamlining genomic research with robust NGS workflow solutions that automate, scale, and integrate bioinformatics tools
AMBER vs GROMACS
Comparing AMBER and GROMACS: Key strengths and best use cases for molecular dynamics simulations
Guide to Loading Genomes in IGV
Explore how to load genome in IGV and how DiPhyx can optimize your IGV projects
Energy Minimization in AMBER
Understanding Amber Relaxation and Energy Minimization in AMBER: A Key Step in Molecular Dynamics