"PACCT 3" : Pairwise Alpha Carbon Comparison Tool for comparison of liganded with Apo- globular protein 3D structures (primarely of α/ß hydrolase fold)

Backbone conformations in X-ray structures  of many PDB deposited α/ß hydrolase fold proteins show surprising similarity among native and liganded forms with typical variability of ~1Å or less to ~2 Å. The largest backbone deviations are frequently observed in their covalent conjugates. Those deviations are likely to influence approach, binding and reaction efficacy of substrates or other ligands.

We developed a novel, reference point based principle for overlay-independent pairwise comparison of liganded and non-liganded Cα conformations from respective PDB structures and encoded it in JAVA based computer algorithm for quick analysis. Comparisons are based on differences in distances between each Cα pair. Distances are calculated either directly between Cα of interest and Cα chosen as a reference point or from differences in the angle between center of mass, reference point and each of Cα in the comparison. Either approach reveals a subset of Cα in two structures that maintains their relative positions in the 3D space best and that can be used as tethering points for overlay of compared structures.