How Our Protein Modelling Service / Homology modeling Service Can Help You ?

The term “homology modeling“, also called comparative modeling or sometimes template-based modelling (TBM), refers to modeling a protein 3D structure using a known experimental structure of a homologous protein (the template). We at RASA follow a comparative modelling routine needing three items of input: The sequence of the protein with unknown 3D structure, the “target sequence“, a 3D template is chosen by virtue of having the highest sequence identity with the target sequence. Structural information is always of great assistance in the study of protein function, dynamics, interactions with ligands and other proteins. The “low-resolution” structure provided by homology modeling contains sufficient information about the spatial arrangement of important residues in the protein and may guide the design of new experiments, for example site-directed mutagenesis. Even within the pharmaceutical industry homology modeling can be valuable in structure-based drug discovery and drug design.

The ab initio prediction methods consist in modelling all the energetic involved in the process of folding, and then in finding the structure with lowest free energy. This approach is based on the ‘thermodynamic hypothesis’, which states that the native structure of a protein is the one for which the free energy achieves the global minimum. While ab initio prediction is clearly the most difficult, it is arguably the most useful approach. There are two components to ab initio prediction: devising a scoring (ie, energy) function that can distinguish between correct (native or native-like) structures from incorrect ones, and a search method to explore the conformational space. In many methods, the two components are coupled together such that a search function drives, and is driven by, the scoring function to find native-like structures.

Threading is also known as Fold Recognition, with this method, you can predict the protein structures of your target protein using known protein folds of similar proteins found in different databases. Online web servers, such as I-Tasser, Phyre2 and others give an insight on working of threading method.