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Quantum Mechanics-Based Fast and Reliable Prediction of Binding Pose Structures.
Al-Ansi, Amar Y; Al-Shawesh, Gamal H; Ru, Xiao; Lin, Zijing.
Afiliación
  • Al-Ansi AY; Department of Physics, University of Science and Technology of China, Hefei 230026, China.
  • Al-Shawesh GH; Department of Physics, Sana'a University, Sana'a, Yemen.
  • Ru X; Hangzhou Nain Biotech Co. Ltd., Hangzhou 310015, China.
  • Lin Z; Department of Physics, University of Science and Technology of China, Hefei 230026, China.
J Phys Chem B ; 128(25): 6059-6070, 2024 Jun 27.
Article en En | MEDLINE | ID: mdl-38875526
ABSTRACT
Predicting the binding poses of docking with an accurate estimation of binding energies is highly important but very challenging in computational drug design. A quantum mechanics (QM) calculation-based docking approach considering multiple conformations and orientations of the ligand is introduced here to tackle the problem. This QM docking consists of three

steps:

generating an ensemble of binding poses with a conventional docking simulation, computing the binding energies with self-consistent charge density functional theory tightly binding with dispersion correction (DFTB-D) to selecting the 10 top binding modes, and optimizing the selected binding mode structures using the ONIOM(DFTBPM7) technique to determine the binding poses. The ONIOM(DFTB-DPM6) docking approach is tested on 121 ligand-receptor biocomplexes with the crystal structures obtained from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). The result shows that the new method is highly satisfactory for the accurate prediction of the binding poses. The new docking method should be beneficial to structure-based drug design.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Teoría Cuántica / Simulación del Acoplamiento Molecular Idioma: En Revista: J Phys Chem B Asunto de la revista: QUIMICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Teoría Cuántica / Simulación del Acoplamiento Molecular Idioma: En Revista: J Phys Chem B Asunto de la revista: QUIMICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos