GeoStaS divides a biomolecule (proteins, nucleic acids and their complexes) into dynamic domains based on its different conformations, obtained from experiments or simulations.
SMOG is a versatile software package for generating structure-based models.SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD.
de Oliveira AB Jr, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. SMOG 2 and OpenSMOG: Extending the limits of structure-based models.
Protein Sci. 2021 Oct 16. doi: 10.1002/pro.4209. Epub ahead of print. PMID: 34655449.
TSN (Top-scoring ‘N’ algorithm) uses a flexible classifier size to expand the permutation and combination space available for classification. TSN relies on an unusual number system known as factoradics to easily translate between permutations of features and decimal numbers.
