ArticleThe journal of physical chemistry. B2021
Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
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- Systematically Improvable and Locality Accelerated Enzymatic Reactivity Modeling: Toward Chemical Accuracy at Affordable Cost.Journal of chemical theory and computation · 2026Article
- Uncertainty Quantification forChemical reviews · 2026Review
- Electric fields enhance Diels-Alderase catalysis in abyssomicin C biosynthesis.Chemical communications (Cambridge, England) · 2026Article
- Quantum Chemistry in Drug Design: Applications, Challenges, and the Need for Speed.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Efficient and accurate spatial mixing of machine learned interatomic potentials for materials science.npj computational materials · 2026Article
- Development of an AMBER-Compatible Force Field for Gold Nanoclusters Protected byJournal of chemical theory and computation · 2025Article
- Hybrid quantum/classical docking of covalent and non-covalent ligands with Attracting Cavities.Scientific reports · 2025Article
- Toward Improving Multiple Time Step QM/MM Simulations with Δ-Machine Learning.The journal of physical chemistry. B · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- SparcleQC: Automated Input File Creation for QM/MM Studies of Protein:Ligand Complexes.Journal of chemical information and modeling · 2025Article
- The ExoGAN generative AI framework enables extracellular vesicle-based immunotherapy.Research square · 2025Article
- Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin-Receptor Interface.Journal of chemical information and modeling · 2025Article
- Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking.Journal of chemical information and modeling · 2025Article
- The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems.Journal of computational chemistry · 2025Article
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM.Journal of chemical theory and computation · 2025Article
- Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions.Journal of chemical theory and computation · 2025Article
- Method and Implementation of Projected Hybrid Orbitals for Treating Multiple Covalent Bonds in Combined QM/MM Calculations.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Electrostatically embedded symmetry-adapted perturbation theory.The Journal of chemical physics · 2024Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.