How do I find (potential) 3D functional sites in a protein structure?
See this Wikiomics article on Searching for 3D functional sites in a protein structure. Some web servers to predict functional sites based on 3D structure Sources: [17] [18] : • SPPIDER – Solvent accessibility based Protein-Protein Interface iDEntification and Recognition • ELM – Functional site prediction • ConSurf – Server for the Identification of Functional Regions in Proteins • CASTp – Computed Atlas of Surface Topography of proteins • PINUP – Protein binding site prediction with an empirical scoring function • Protein-Protein Interaction Server • InterPreTS – Prediction of the potential interaction of two proteins from their sequences • PPI-Pred – Protein-Protein Interface (Binding Site) Prediction • ProMate – Predicting the location of potential protein-protein binding sites for unbound proteins • PRISM – protein interactions by structural matching • PI2PE – cons-PPISP for finding protein-protein interfaces, or DISPLAR for protein-dna interfaces And it is always useful to visit
