PocketAnnotate is a computational pipeline, for facilitating functional annotation of proteins at the level of ligand binding sites. With a structural model as input, PocketAnnotate processes it in three different phases: (a) by identifying ligand binding sites, (b) fast comparison of identified pockets to a database of known ligand-binding sites (c) detailed alignment of high scoring site-pairs. Through these steps, one can obtain clues about possible ligands that can bind to a query protein and hence infer its function. A structure based function annotation at the level of binding sites can be achieved and this pipeline could prove very useful for cases where no obvious functional inference can be obtained based purely on sequence or motif analyses.



PocketAnnotate can be used in three ways based on the extent of information available about binding site




Please select the type of query   Query Type
Three types of query can be submitted, it can either be protein-ligand complex, only protein or just the substructure of a protein





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Enter PDB ID: (Eg-1A4G) Chain ID: (A-Z)  
You should enter unique 4 letter PDB code found in RCSB Database

Upload   PDB File
Upload only PDB format file containing the ATOM cooridnates only

(Please upload a structure containing not more than four chains.)





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