ArticleAdvances in bioinformatics2017
Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.
Article in Advances in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- SMILES2Docking: An Open-Source Desktop Workflow for Ligand Ionization, Stereochemistry-Aware Preparation and Semi-Empirical 3D Refinement.Molecular informatics · 2026Article
- Article
- Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations.Nanomaterials (Basel, Switzerland) · 2022Article
- Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors.ACS omega · 2021Article
- Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations.Frontiers in molecular biosciences · 2021Article
- High-Throughput Docking Using Quantum Mechanical Scoring.Frontiers in chemistry · 2020Article
- In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4.Viruses · 2019Article
- Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.ACS omega · 2017Article
- Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.Computational and structural biotechnology journal · 2017Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
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Registered trials
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