Computational Programs for Pocket Detection in Proteins

 Active site pockets in proteins are specific regions of the protein structure where chemical reactions take place. These pockets contain specific amino acids that interact with substrate molecules and catalyze chemical reactions. They are often located in the interior of the protein and are protected from the surrounding environment, allowing the protein to selectively bind to specific substrate molecules and perform specific chemical reactions. Active site pockets are an important target in drug discovery, as they can be targeted by small molecules to modulate protein function and treat various diseases.

There are several computational tools that can be used for protein active pocket detection:

Molecular docking: Predicts how a small molecule will bind to a protein active site. There are a variety of docking programs available both commercial and for academic purposes (free), like AutoDock and  AutoDock Vina.

SiteFinder: Predicts protein binding sites using a knowledge-based scoring method. You can use or download the program from PEP-SiteFinder

Phase: Predicts active sites using a pharmacophore model and 3D-QSAR analysis. Phase

ConCavity: Detects pockets in protein structures using a cavity detection algorithm. ConCavity

FPocketWeb: Predicts protein pockets using a combination of shape and electrostatic complementarity analysis. Fpocketweb

PDBbind: A database of protein-ligand complexes that can be used for active site prediction and analysis. PDBBind

Vina: A molecular docking program that predicts the binding affinity of a ligand to a protein.

These tools can be useful in the drug discovery process for identifying potential drug targets and predicting the binding of small molecules to protein active sites.