Explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric unit of the same protein in PDB. PDBFlex allows to easily identify regions and types of structural flexibility present in a protein of interest. Structures of protein chains with identical sequences (sequence identity > 95%) were aligned, superimposed and clustered. Then global and local structural differences were calculated within these clusters. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software.