Molecular_cradle

A package to identify almost rigid regions in complex biomolecules Reference Manual – User Manual . Authors: M. Simsir and F. Cazals

Main classes:

• SBL.Molecular_cradle_step1.Cradle_step1 : Compute distances (lRMSD or RMSDcomb) for given pdb files and perform a hierarchical clustering.

• SBL.Molecular_cradle_step2.Cradle_step2 : Get subdomain average Mean displacement, compute distances (lRMSD or RMSDcomb) for given pdb files with different spec files, and perform a hierarchical clustering.

• SBL.Molecular_cradle_step2_selected.Cradle_step2_selected : Compute distances (lRMSD or RMSDcomb) for given pdb files and perform a hierarchical clustering.

• SBL.Molecular_cradle_step3.Cradle_step3 : Compute interfaces for given pdb files for every specified subdomains.

• SBL.Molecular_cradle_utils_dendogram.Matrix_processor : Write matrix N x N of all distances between monomers from pairewise comparisons.

• SBL.Molecular_cradle_utils_dendogram.Dendogram_processor : Perform hierachical clustering

• SBL.Molecular_cradle_utils_distance.Distance_calculator : Compute distances (lRMSD or RMSDcom) for given pdb files following given spec files.

• SBL.Molecular_cradle_utils_label_selection.Label_selector : Selection of subdomains which are dynamic, see paper