Apps

Apps

Open tools we develop for building and designing nucleic-acid systems for molecular simulations. Each app lives in its own GitHub repository.

dsXNAbuilder

Double-stranded DNA, RNA and DNA/RNA builder with modXNA chemistry.

Generates canonical double-stranded (ds) DNA, RNA and DNA/RNA hybrid sequences, combining the canonical bases with the modified nucleotides available in modXNA, the modified-nucleic-acid library we co-develop.

  • dsDNA, dsRNA and DNA/RNA hybrids
  • Canonical and modXNA-modified nucleotides
  • Ready-to-use input for molecular simulations
Launch app

panmer

Sequence-library generator for molecular dynamics, with the expanded modXNA alphabet.

Designs libraries of DNA and RNA sequences for molecular dynamics (MD) simulations, supporting the expanded alphabet of modXNA. It is based on the Orenstein & Shamir algorithm for designing compact sequences that cover every k-mer.

  • DNA and RNA sequence libraries
  • Expanded modXNA alphabet
  • Based on the Orenstein & Shamir algorithm
Launch app