Computational protocol: Conformational diversity analysis reveals three functional mechanisms in proteins

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Protocol publication

[…] Hinges were detected with FlexProt [], the number of hinges identified maximizes the structural superposition between conformers. The Radius of gyration (Rg) of each conformer was calculated using the MMTSB Tool Set (available from http://blue11.bch.msu.edu/mmtsb/). Due to the dependence of Rg with protein size, a normalized Rg was calculated from the Rg of the ideal sphere of the same volume of the protein structure [].Pockets were detected with FPocket [], using the highest scored pocket. The percentage of maximum variation between maximum pocket volumes (with/without IDRs residues) in each conformer was calculated as |max(pV1,IDR, pV2,IDR) − max(pV1, pV2)|/max(max(pV1,IDR, pV2,IDR), max(pV1, pV2)), where pVi is the pocket volume (with/without IDRs residues) on the corresponding conformer. MOLE 2.0 [] was used for tunnel identification and characterization using the following parameters. Probe Radius and Origin Radius 3 Å, Interior Threshold 1.25 Å and default values for all the others. We parsed the XML file output to identify tunnel length, number of tunnels, residues lining each tunnel and so on. The proportion of variation between largest tunnels in each conformer was calculated as |L1 − L2 |/max(L1,L2), where Li is the length of the largest tunnel on the corresponding conformer in the maximum pair. The protein volume was estimated by 3vee [] using a probe radius of 0.5 Å and a grid resolution of 1.5 Å. Residue interactions networks (RINs) were built with RING []. […]

Pipeline specifications

Software tools FlexProt, fpocket
Application Protein structure analysis