Molecular biology visualization examples

Mechanisms drawn and animated by Molecular Motion. Each one is a single YAML file in the repository, which you can open in the playground and change.

Explained step by step

DNA repair

Base excision repair of an oxidized base, and how PARP1 signals the single-strand break it leaves behind, as an animated SVG figure you can step through. The whole figure is generated from one YAML file.
Protein–DNA interactions

Proteins that bind, coat and leave a stretch of DNA, drawn where they sit on the molecule. The example is the repair of a double-strand break by homologous recombination, from the break to an intact chromatid.
Gene expression

A gene is transcribed into RNA, the intron is spliced out, and the mRNA reaches a ribosome in the cytoplasm. The transcript grows nucleotide by nucleotide on its template, and loses its intron without being redrawn as a new molecule.
Membrane receptor signalling

A receptor in a lipid bilayer binds its ligand outside the cell, dimerizes, and is phosphorylated inside it. The example is the activation of the EGF receptor, with every receptor and ligand drawn as an individual copy.
Cell signalling

A signal followed from its trigger to the nucleus: DNA in the cytosol, a second messenger, a membrane protein that changes compartment, a kinase and a transcription factor. The example is the cGAS–STING pathway of innate immunity.

A negative feedback loop

p53 turnover, the stress response and induction of its inhibitor MDM2.
Double Holliday junction

Second-end capture and resolution as a crossover by reconnecting strands.