ArticleMolecules (Basel, Switzerland)2021
Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- TLR2 c.374C>T variant linked to natural resistance against brucellosis in Italian Mediterranean river buffalo.BMC veterinary research · 2025Article
- Optimization of lipase activity in Aspergillus niger C2J6 whole cells using choline chloride ethylene glycol deep eutectic solvent.Scientific reports · 2025Article
- Article
- Article
- Current developments and trends in quantum crystallography.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2024Article
- The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method.The journal of physical chemistry. B · 2022Article
- Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB.Journal of chemical information and modeling · 2022Article
- Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank.Acta crystallographica. Section D, Structural biology · 2022Article
- Electron density is not spherical: the many applications of the transferable aspherical atom model.Computational and structural biotechnology journal · 2022Review
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2 authors.
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Abstract
Computational analysis of protein-ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions, such as in docking programs, all rely on equations that sum each type of protein-ligand interactions in order to predict the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions constitute one of the most important part of total interactions between macromolecules. Unlike dispersion forces, they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this study, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and darunavir) were analyzed by using charge densities from the transferable aspherical-atom University at Buffalo Databank (UBDB). Moreover, we analyzed the electrostatic interaction energy for an ensemble of structures, using molecular dynamic simulations to highlight the main features of electrostatic interactions important for binding affinity.
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