Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 57, Issue 7, Pages 1715-1721Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.7b00226
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Funding
- NSF [IIS-1302285, DMS-1721024]
- MSU Center for Mathematical Molecular Biosciences Initiative
- Div Of Information & Intelligent Systems
- Direct For Computer & Info Scie & Enginr [1302285] Funding Source: National Science Foundation
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Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug and protein design. Based on large scale data sets, we show that protein rigidity strengthening or flexibility reduction is a mechanism in protein-ligand binding. Our approach based solely on rigidity is able to unveil a surprisingly apparently long-range contribution of apparently four residue layer to protein-ligand binding, which has ramifications for drug and protein design. Additionally, the present work reveals that among various pairwise interactions, the short-range ones within the distance of the van der Waals diameter are most important. It is found that the present approach outperforms all other state-of-the-art scoring functions for protein-ligand binding affinity predictions of two benchmark test sets.
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