Chiron
Minimizes steric clashes in protein structures using short DMD simulations. Preserves backbone conformation while resolving atomic overlaps from homology models, low-resolution structures, and cryo-EM maps.
Gaia
Evaluates protein structure quality against high-resolution crystal benchmark data, providing per-metric p-values for clashes, hydrogen bonds, voids, geometry, and side chains.
Citation
Ramachandran, S., Kota, P., Ding, F. and Dokholyan, N. V.
“Automated minimization of steric clashes in protein structures”
Proteins: Structure, Function and Bioinformatics (2011)
DOI: 10.1002/prot.22879 · PMID: 21058396