Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems
Published 2022 View Full Article
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Title
Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems
Authors
Keywords
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Journal
DRUG DISCOVERY TODAY
Volume 28, Issue 1, Pages 103374
Publisher
Elsevier BV
Online
2022-09-27
DOI
10.1016/j.drudis.2022.103374
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- (2021) Ernest Awoonor-Williams et al. Journal of Chemical Information and Modeling
- Tuning the Quantum Chemical Properties of Flavins via Modification at C8
- (2021) Rajiv K. Kar et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Towards reproducible computational drug discovery
- (2020) Nalini Schaduangrat et al. Journal of Cheminformatics
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- (2020) Kamonpan Sanachai et al. ACS Omega
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- (2020) Johannes C. B. Dietschreit et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Elucidating the Molecular Basis of Avibactam Mediated Inhibition of Class A β-Lactamases
- (2020) Chandan Kumar Das et al. CHEMISTRY-A EUROPEAN JOURNAL
- Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)
- (2020) Ryo Hatada et al. Journal of Chemical Information and Modeling
- TeraChem : A graphical processing unit ‐accelerated electronic structure package for large‐scale ab initio molecular dynamics
- (2020) Stefan Seritan et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces
- (2020) Gerhard König et al. Interface Focus
- End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
- (2019) Ercheng Wang et al. CHEMICAL REVIEWS
- Energy Decomposition Analysis of Protein-Ligand Interactions Using Molecules-in-Molecules Fragmentation-Based Method
- (2019) Bishnu Thapa et al. Journal of Chemical Information and Modeling
- Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD: A tutorial review
- (2018) Shideh Ahmadi et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- Markov State Models: From an Art to a Science
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- Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
- (2018) Rommie E. Amaro et al. Nature Reviews Chemistry
- Assessing the Performance of MM/PBSA, MM/GBSA, and QM–MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions
- (2018) Sushil K. Mishra et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
- (2018) Isabella A. Guedes et al. Frontiers in Pharmacology
- Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment
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