ArticleAdvances in bioinformatics2015
Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima.
Article in Advances in bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Improving drug-induced liver injury prediction using graph neural networks with augmented graph features from molecular optimisation.Journal of cheminformatics · 2025Article
- Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations.Nanomaterials (Basel, Switzerland) · 2022Article
- Potential activity of Linezolid against SARS-CoV-2 using electronic and molecular docking study.Journal of molecular modeling · 2021Article
- Are losartan and imatinib effective against SARS-CoV2 pathogenesis? A pathophysiologic-based in silico study.In silico pharmacology · 2021Article
- Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach.International journal of biological macromolecules · 2020Article
- Article
- Synergistic Effects of Curcumin and Piperine as Potent Acetylcholine and Amyloidogenic Inhibitors With Significant Neuroprotective Activity in SH-SY5Y CellsFrontiers in aging neuroscience · 2019Article
- Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.ACS omega · 2017Article
- Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.Journal of molecular graphics & modelling · 2017Article
- Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.Computational and structural biotechnology journal · 2017Article
- Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.Advances in bioinformatics · 2017Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.
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