Resources
RESOURCES
Tools and Resources
Software, datasets, and links of varying usefulness.
Software
NARestraints
Used for non-canonical nucleic acid crystallgraphy, plugging into Phenix environment.
Infers secondary structure using antiparallel run model. Then generates restraints for WC, WC-like, GU wobble, and AG Hoogsteen pairs based on phenix library. Employs ligand library compiled by Wang, Guo and Vecchioni to screen atom names for bond and angle generation. Tolerant to mislabeled atoms.
Further generates stacking restraints for modified residues.
Finally, contains tool to coordinate flip DNA and RNA into enantiomers, with support for atom and residue names.
Linking Number and other Differential Geometry
Linking number calculator for Matlab, which processes PDB files of DNA tiles. It was developed for our paper on tertiary chirality in 2023: Janowski, J. et al, “Engineering Tertiary Chirality in Helical Biopolymers.” PNAS 121(19), e2321992121 (2024)..
External resources
Protein Databank (PDB)
Biomolecular structure repository with more than just proteins.
PDB Molecule of the Month
Curated examples of molecular families, including the RNA cages linked here.
Web 3DNA
Structural analysis of nucleic acids, mostly functional.