This module is for the occasion where a annotated SNP is available, but it has not been mapped onto a PDB structure yet. There is also no specific drug molecule of interest. The user wants to get a rapid prediction regarding the binding affinity change to evaluate the possibility that this SNP would cause drug-resisgence upon the protein that it would mutate with a drug ligand molecule. To run this module, SIFT, PolyPhen-2, GERP score regarding the target SNP is required. The user also need to indicate whether this SNP will be mapped onto a amino acid that is within the binding pocket or not.
This module is for the occasion that the annotated SNP is available, and you also have a PDB structure that this SNP is mapped onto. But there is no drug ligand modecule present in the PDB structure. With the information of wildtype amino acid and mutated aminoacid, more features regarding the aminoacid would be feed into GenoDock to get binding affinity change prediction.
This module is designed for the occasion that there is a particular drug ligand of interest together with the annotated SNP available. Here the user is driven to investigate whether this SNP would casue drug-resistance regarding a specific drug molecule. No PDB structure information is required for this module. For a query of properties of target drug ligand as input arguments (molecular weight, polar surface area, etc.) of this module, please refer to the PubChem Compound website.
This is the most comprehensive module in GenoDock in terms of information feeding. The user have a co-crystal PDB file available so that there is a known protein and a known drug ligand molecule around it. Together with the annotated SNP, GenoDock would perform yet the most reliable prediction upon the binding affinity change within the 4 modules. For a query of properties of target drug ligand as input arguments (molecular weight, polar surface area, etc.) of this module, please refer to the PubChem Compound website.