Docking

Computational docking is a modeling 3D tool for protein-ligand complexes.

CAPRI

ab initio docking

ab initio, non-template or free modeling There are several different “ab initio” in bioinformatics, e.g.:

• ab initio protein folding
• ab initio gene prediction
• ab initio genome assembly And so on. In general, ab initio in bioinformatics means “without direct evidence”. For example, ab initio genome assembly is assembling a genome from sequencing reads alone, without any other information like a closely related genome or a genetic map.

Template-based modeling (TBM)

Is a very reliable alternative to ab initio docking, given that a template is available. With a template many approaches can be used, including:

1. ‘(global) superimposition’ (i.e. global structure–structure alignment), generating models by superimposing unbound 3D component protein (or domain) structures onto templates;
2. ‘dimeric threading’ (i.e. sequence–structure alignment), ‘threading’ the component protein sequences onto structural templates and searching for the best sequence–structure alignment based on a scoring function;
3. ‘direct homology modeling of the complex’, e.g. with MODELLER;
4. ‘Interface Structure Alignment’ (ISA)based modeling, generating models by superimposing the component protein structures onto template interface structures.