Molecular simulation is a method of using computers to simulate molecular structure and behavior with atomic-level molecular models, various physical and chemical properties of molecular systems can be obtained with this technology. It builds a set of models and algorithms based on experiments and basic principles to calculate reasonable molecular structures and molecular behaviors. Molecular simulation approach can simulate not only the static structure of molecules, but also the dynamic behavior of molecular systems. There are two main methodologies applied in molecular simulation: Quantum mechanics simulation and classical mechanics simulation. In the field of new drug development, molecular simulation technology can be used to predict the binding of small molecules to protein targets and calculate the binding affinity to support the discovery and structural optimization of lead compounds.
Figure 1. (A) Structure of oncostatin M (OSM); the modeled fragments are colored in red. (B) Sequence alignment between oncostatin M receptor (OSMR) and leukemia inhibitory factor receptor (LIFR). (C) Structural alignment of OSMR homology model (red) and LIFR crystal structure (green). (D) Docking funnel of OSM and OSMR. (Du, Q.; et al. 2020)
Application of Molecular Simulation in Drug Design
- Simulate the solubility of drugs
- Study the interaction between drugs and targets
- Drug molecule crystal structure prediction
Molecular Simulation Methodologies
The main simulation methods of molecular simulation are quantum mechanics simulation and classical mechanics simulation.
- Quantum mechanics simulation
Ab initio calculation
Density functional theory (DFT) method
- Mechanics simulation method
Monte Carlo simulation
Alfa Chemistry provides easy-to-use protein simulation, drug design and optimization tools for protein structure and function studies. Our rapid and high-quality services is as follows:
- Biological macromolecules
We provide protein/nucleic acid sequence analysis, protein evolution analysis, 3D structure prediction and simulation, protein structure surface charge analysis and pKa value prediction, membrane protein structure prediction and simulation, antibody design and analysis, protein rational design, protein aggregation effect prediction, nucleic acid design and simulation, protein (nucleic acid)-protein (nucleic acid) interaction, etc.
- Structure-based drug design
Our teams can perform ligand-target interaction (molecular docking), structure-based virtual screening, fragment-based drug design, etc.
- Ligand-based drug design
Alfa Chemistry supports pharmacophore design based entirely on ligand/ligand-receptor complex, construction and screening of compound database, quantitative structure-activity relationship (QSAR/QSPR) analysis, structure-activity relationship (SAR) analysis, virtual combinatorial chemical library design and analysis, drug-like screening, compound conformation search and analysis, ADMET prediction, etc.
- Computational chemistry
We use the CHARMm calculation engine and the CHARMm series of force fields to simulate a variety of Poisson-Boltzmann (PB) and Generalized Born (GB) types of invisible solvent models, CFF or MMFF force field and several other optimization algorithms for in-situ ligand optimization, ab initio calculation for ligands or small organic molecules studies, molecular dynamics trajectory studies, conformation and energy calculation at the binding site, support parallel calculation.
Features of Our Molecular Simulation
- Our multi-scale and multi-functional molecular simulation platform integrates various simulation methods, enabling full-scale scientific research from electronic structure analysis to macroscopic performance prediction.
- Applications of our molecular simulation services cover the three disciplines of medicine, chemistry, and biology, providing comprehensive support for new drug discovery and design.
- High-quality graphical interface, scientific algorithms proven for many years, and integrated environment.
Our molecular simulation services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!
- Du, Q.; et al. Molecular Simulation of Oncostatin M and Receptor (OSM-OSMR) Interaction as a Potential Therapeutic Target for Inflammatory Bowel Disease. Frontiers in Molecular Biosciences. 2020, 7.