Читать книгу Computation in BioInformatics - Группа авторов - Страница 16

If a drug that needs to bind to a particular on a particular protein or nucleotide is known, then it can be tailor made to bind at that site. This is often performed computationally using several different techniques. Traditionally, the primary way is to identify compounds which can interact with the specific molecular site responsible for the disease. A second method is to test the specific compound against various molecular sites known for the occurrence of the disease. However, if the 3D structure of the protein target is not available, then the method of molecular modeling needs to be performed in order to construct the structure for further analysis.

 CASTp: Computed Atlas of Surface Topography of proteins (CASTp) is an online resource which is used for locating, delineating and measuring of concave surface regions on the 3D structures of protein [13]. It includes pockets which are located on protein surfaces. This server can be used to study surface features and functional regions of proteins. The server is updated daily and can be accessed at http://cast.engr.uic.edu

 Active Site Prediction Server: Active Site Prediction of Protein server help in computing the cavities in a given target protein. This sever can be easily accessed at http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp.

 3DLigandSite: It is an automated method which can predict the ligand binding sites. One can submit a sequence or a protein structure and once submitted Phyre is run to predict the structure. The structure can then be used to search a structural library in order to identify homologous structures with bound ligands. These ligands are then superimposed onto the protein structure in order to predict a ligand binding site [14]. It can be accessed at http://www.sbg.bio.ic.ac.uk/3dligandsite.