ArticleMethods in molecular biology (Clifton, N.J.)2019
Force Fields for Small Molecules.
Article in Methods in molecular biology (Clifton, N.J.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Insights into the Possible Impact of PFAS on Phosphatidylcholine Metabolism and Membranes through Molecular Dynamics Simulations.ACS environmental Au · 2026Article
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- CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Modeling and Simulations.Journal of chemical information and modeling · 2026Article
- Integrating Molecular Dynamics Simulations and Single-molecule FRET Spectroscopy: From Computational FRET Estimation to Experimental Data Interpretation.The journal of physical chemistry. B · 2026Review
- Natural Fatty Acids as Dual ACE2-Inflammatory Modulators: Integrated Computational Framework for Pandemic Preparedness.International journal of molecular sciences · 2025Article
- Augmentation of antibacterial activity of ciprofloxacin by bisabololoxide A encapsulated in polymeric nanoparticles against uropathogenic Escherichia coli.BMC biotechnology · 2025Article
- Unveiling molecular moieties through hierarchical Grad-CAM graph explainability.BMC bioinformatics · 2025Article
- Histidine Focused Covalent Inhibitors Targeting Acetylcholinesterase: A Computational Pipeline for Multisite Therapeutic Discovery in Alzheimer's Disease.ACS chemical neuroscience · 2025Article
- Predicting Distribution Coefficients (LogD) of Cyclic Peptides Using Molecular Dynamics Simulations.Pharmaceutical research · 2025Article
- Multiple Topology Replica Exchange of Expanded Ensembles for Multidimensional Alchemical Calculations.Journal of chemical theory and computation · 2025Article
- Structural basis for antibiotic transport and inhibition in PepT2.Nature communications · 2024Article
- Review
- Transferable Machine Learning Interatomic Potential for Bond Dissociation Energy Prediction of Drug-like Molecules.Journal of chemical theory and computation · 2024Article
- High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Carbon Nanodots from an In Silico Perspective.Chemical reviews · 2022Review
- Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.Journal of chemical theory and computation · 2022Article
- AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials.Scientific data · 2022Article
- Recent progress in general force fields of small molecules.Current opinion in structural biology · 2022Review
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2 authors.
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Abstract
Molecular dynamics (MD) simulations have been widely applied to computer-aided drug design (CADD). While MD has been used in a variety of applications such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also act as model compounds that will be transferred to ligands used in CADD. Currently, a wide range of small molecule force fields based on additive or nonpolarizable models have been developed. While these nonpolarizable force fields can produce reasonable estimations of physical properties and have shown success in a variety of systems, there is still room for improvements due to inherent limitations in these models including the lack of an electronic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polarizable force fields are able to provide a better physical representation of intermolecular interactions and, in many cases, better agreement with experimental properties than nonpolarizable, additive force fields. Therefore, this chapter focuses on the development of small molecule force fields with emphasis on polarizable models. It begins with a brief introduction on the importance of small molecule force fields and their evolution from additive to polarizable force fields. Emphasis is placed on the additive CHARMM General Force Field and the polarizable force field based on the classical Drude oscillator. The theory for the Drude polarizable force field and results for small molecules are presented showing their improvements over the additive model. The potential importance of polarization for their application in a wide range of biological systems including CADD is then discussed.
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