Daedalus

View proteins and other molecules in 3D, with an easy-to-use interface, and fast performance. View electron density, and perform molecular dynamics. Sophisticated molecular docking capabilities. Open source.

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PlasCAD

View and edit plasmids for molecular bio workflow. Design and validate primers. Miscellaneous tools for molecular biologists. Open source.

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Biology libraries for Rust and Python applications

We provide foundational libraries for structure biology in Rust. These provide functionality that are common in Python and other languages, but were unavailable to Rust applications. We also include Python bindings for all of these.

• Dynamics. Perform molecular dynamics using Amber force fields. Easy to install and use, customizable, and supports common molecule formats directly.
• Bio Files. Read and write mmCIF, Mol2, SDF, Map, AMBER parameters, and other common biology file formats. Includes reusable data structures for molecules, bonds, atoms, and more.
• NA Seq. Biology fundamental sequence primitives and tools. Provides fundamental types for nucleic acids, amino acids, elements, and more. Tools for [de]serializing them from common representations, and computations.
• Bio APIs. Interact with the RCSB PCB API, PubChem, DrugBank, NCBI Blast, and our own library of AMBER Geostd MOl2 and FRDMOD files for small organic molecules.
• Ewald SPME. Run Smooth Particle Ewald Mesh (SPME) computations to calculate Coulomb force with many bodies, under periodic boundary conditions. This is a standard molecular dynamics algorithm.
• Marching Cubes: Isosurfaces. Generate isosurfaces from volumetric data. Useful for viewing and performing computations on Cryo-EM and crystallography data, and computing solvent-accessible-surfaces.