"Applications of Molecular Dynamics Simulations in Drug Discovery"

‍◦ DOI: 10.1007/978-1-0716-3441-7_7

‍◦ Summary: Provides an overview of the current applications of MD simulations in drug discovery, including detecting protein druggable sites, validating drug docking outcomes, and exploring protein conformations.

"Molecular Dynamics (MD) Simulations Provide Insights into the Activation Mechanisms of 5-HT2A Receptors"

‍◦ Publication Date: 2024-10-01

◦ DOI: 10.3390/molecules29204935

‍◦ Summary: Characterizes protein dynamics of the 5HT2A receptor stimulated by ligands using 1 µs MD simulations, providing insights into receptor activation mechanisms.

"Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development"‍

◦ Publication Date: 2020-12-30

◦ DOI: 10.3390/pr9010071◦ Summary: Reviews the current application possibilities of MD in drug discovery and pharmaceutical development, including target validation, lead discovery, and pharmaceutical formulation development.

"From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery"

‍◦ Publication Date: 2023-12-29

◦ DOI: 10.1186/s12915-023-01791-z

‍◦ Summary: Discusses how MD simulations have advanced to become powerful tools for investigating dynamic interactions between potential small-molecule drugs and their target proteins.

"Role of Molecular Dynamics and Related Methods in Drug Discovery"‍

◦ Publication Date: 2016-02-08

◦ DOI: 10.1021/acs.jmedchem.5b01684

‍◦ Summary: Reviews the theoretical background of MD and enhanced sampling methods, focusing on free-energy perturbation, metadynamics, steered MD, and other methods used to study drug-target binding.

"Discovery of a Heparan Sulfate Binding Domain in Monkeypox Virus H3 as an Anti-Poxviral Drug Target Combining AI and MD Simulations"‍

◦ Publication Date: 2024-11-27

◦ DOI: 10.7554/eLife.100545

‍◦ Summary: Combines AI-based structural prediction tools and MD simulations to identify a novel domain in MPXV H3 protein, leading to the design of a protein inhibitor that disrupts viral adhesion.

"Molecular Dynamics Simulations in Drug Discovery and Drug Delivery"

‍◦ DOI: 10.1007/978-3-030-36260-7_10

‍◦ Summary: Discusses the role of MD simulations at different stages of the drug discovery process and how they aid in understanding molecular systems.

"Molecular Docking, ADMET Analysis and Molecular Dynamics (MD) Simulation to Identify Synthetic Isoquinolines as Potential Inhibitors of SARS-CoV-2 MPRO"‍

◦ Publication Date: 2023-01-23

◦ DOI: 10.2174/1573409919666230123150013

‍◦ Summary: Integrates molecular docking, ADMET analysis, and MD simulations to identify isoquinoline derivatives as potential inhibitors of SARS-CoV-2 MPRO.

"Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography"‍

◦ Publication Date: 2023-04-22

◦ DOI: 10.1021/acs.jcim.3c00236

‍◦ Summary: Uses long-timescale MD simulations to discover binding poses for fragments in allosteric pockets on PTP1b, validated by X-ray crystallography.

"Recent Insights from Molecular Dynamics Simulations for GPCR Drug Discovery"

‍◦ Publication Date: 2019-08-29

◦ DOI: 10.3390/ijms20174237

‍◦ Summary: Highlights recent MD simulation studies and enhanced sampling methods used to study biased GPCR signaling and their conformational dynamics.

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