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Home Discovery CRO Molecular Dynamics Simulation

Molecular Dynamics Simulation

Molecular dynamics (MD) as a part of structure-based drug design plays a crucial role in modern drug discovery by providing insights into the behavior and interactions of biomolecules at the molecular level. By solving Newton's equations of motion, MD generates trajectories for all atoms in the system, enabling the computation of various properties. As a result, this vital data is used for designing and optimizing drug candidates with high specificity and efficacy. Molecular Dynamics Simulation Schema Molecular Dynamics Simulation Schema Here at Chemspace, we offer a wide range of MD simulation services applicable to the proteins and the protein-ligand complexes to give important insights into the dynamics and function of the targets and facilitate the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development.

Simple Protein MD Simulation Studies

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The challenge of incorporating the protein's structural flexibility is one of the most critical limitations in structure-based drug design.
By simulating the movement and behavior of atoms within a protein structure we offer:
  • Finding the correct conformation and estimation of conformation stability;
  • 4D structures: building the ensemble of pocket conformations for molecular docking;
  • Assessing side chain modality.
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MD for investigating Ligand Binding

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MD coupled with enhanced sampling methods serves as a pivotal method for studying the dynamic interactions and behaviors of protein-ligand systems. It enables the exploration of the structural changes induced by ligand binding and energetic fluctuations within the protein-ligand complex, offering valuable insights into the stability and affinity of the complex.
We offer:
  1. Steered MD. This method can be used as a rapid postprocessing tool for discriminating active and inactive binders by simply analyzing the SMD-derived force profiles related to ligand unbinding simulations [1].
  2. Absolute and relative binding free energy (A/RBFE). By using AToM-OpenMM software binding free energies can be accurately computed thus boosting lead optimization in structure-based drug discovery [2].

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  1. De Vivo, M.; Masetti, M.; Bottegoni, G.; Cavalli, A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J. Med. Chem. 2016, 59 (9), 4035–4061. https://doi.org/10.1021/acs.jmedchem.5b01684 .
  2. Sabanés Zariquiey, F.; Pérez, A.; Majewski, M.; Gallicchio, E.; De Fabritiis, G. Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. J. Chem. Inf. Model. 2023, 63 (8), 2438-2444. https://doi.org/10.1021/acs.jcim.3c00178 .