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Protein-ligand binding is essential to almost all life processes. Theunderstanding of protein-ligand interactions is fundamentally important torational drug design and protein design. Based on large scale data sets, weshow that protein rigidity strengthening or flexibility reduction is a pivotingmechanism in protein-ligand binding. Our approach based solely on rigidity isable to unveil a surprisingly long range contribution of four residue layers toprotein-ligand binding, which has a ramification for drug and protein design.Additionally, the present work reveals that among various pairwiseinteractions, the short range ones within the distance of the van der Waalsdiameter are most important. It is found that the present approach outperformsall the other state-of-the-art scoring functions for protein-ligand bindingaffinity predictions of two benchmark data sets

Rigidity strengthening is a vital mechanism for protein-ligand binding