7. Provide detailed description for model building
All the steps of the modelling
procedure should be provided. For that purpose, provide information
about the program(s) used, including version number. All the options and
parameters used to adjust the program have to be included. Describe how
amino acid substitutions were implemented. If loops have been modelled,
provide information for algorithm, databases and program parameters. The
approach used for building loops can have substantial effect on model
quality and applicability.
If any manual steps are included, describe how they have been
implemented and justify the choices made.
Example: The structure was modelled with program MODELLER (10.0,
released Feb. 2nd, 2021 (MartÃ-Renom et al., 2000)) using UCSF Chimera
(1.15) (Pettersen et al., 2004) interface. The Dunbrack 2010 rotamer
library (Shapovalov and Dunbrack, 2011) was used to model substitutions
to fit the sidechains into the structure with typical rotamer angles.
Deletions and insertions were modelled based on the sequence alignment
by replacing an existing loop or connecting segment. DOPE - Discrete
Optimized Protein Energy score (Shen and Sali, 2006) with Lennard-Jones
potential and GB/SA implicit solvent interaction was used for loop
building.