3dligandsite: is an automated method for the prediction of ligand binding sites.

PLIP: Protein-Ligand Interaction Profiler

Poseview on-line

LIGPLOT: Program for automatically plotting protein-ligand

MESPEUS:Metal Sites in Proteins - MESPEUS database

MIPS:Metal Interactions in Protein Structures

The Ligand Binder: helps the user generate a series of CHARMM inputs to calculate a protein/ligand binding free energy.

PoseView: automatically generates high-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. Such input may come directly from crystal structures or be computed for example by a docking program.

MetalPDB collects and allows easy access to the knowledge on metal sites in biological macromolecules, starting from the structural information contained in the Protein Data Bank (PDB)

Pocketmatch:Usage of this web interface: Two PDB files whose ligands need to be compared are obtained from the upload. Each of the protein files is then processed to extract all ligands and their corresponding site files. All vs All comparison of sites is done with PocketMatch and scores are reported.

webPIPSA: Protein Interaction Property Similarity Analysis

list of software for pocket characterization