Computational docking can be used to predict the binding conformation and binding free energy of small molecules to proteins. Docking is widely used in the study of protein interactions and mechanisms, and in structure-based drug design. With years of experience, we provide customized molecular docking service to precisely meet customer requirements.

Introduction of Molecular Docking

Molecular docking is a type of bioinformatics modeling by studying molecules with proteins to form stable complexes with potential efficacy and higher specificity. Associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates and lipids play a central role in signal transduction. Therefore, docking is very useful for predicting the strength and type of signal produced. In addition, molecular docking has become the most widely used virtual screening method to predict the binding affinity between ligands and proteins and the structure of protein-ligand complexes.

Fig 1. A typical docking workflow. (Stanzione F, et al., 2021)

Services

The tertiary structure of proteins is necessary to understand the binding modes and affinities between interacting molecules. However, obtaining complex structures through experimental methods such as X-ray crystallography or NMR is often difficult and expensive. Therefore, computational-based molecular docking has become a key tool in structural molecular biology and computer-aided drug design. As a leading service provider of protein engineering, Creative BioMart has successfully developed programs based on different algorithms for molecular docking studies to accurately predict binding conformations between ligands and proteins. We can provide docking services between a variety of ligands and proteins:

• Protein-Nucleic Acid Docking
• Antibody-Antigen Docking
• Protein-Ligand Docking
• Protein-Protein Docking
• Protein-Peptide Docking
• Protein-Carbohydrate Docking
• Protein-Lipid Docking

Firstly, the 3D protein structure is obtained by experimental methods or protein structure model construction. This 3D structure and the prepared ligand database can be used as the input of the molecular docking program. The success of the docking procedure relies on two components: the search algorithm and the scoring function. Our scientists mainly use the following two methods for molecular docking, and significant progress has been made in the computational prediction of docking patterns.

• Simulation method: the ligand and target are separated by a physical distance, and the ligand is then allowed to bind to the groove of the target after "moving a certain number of times" in its conformational space.
• Shape complementary method: this approach employs ligands and targets as surface structural features, providing their molecular interactions

Applications of Molecular Docking

• Lead optimization.
• Hit identifications.
• Drug-DNA interaction.

Creative BioMart is committed to providing global customers with high-quality molecular docking services to predict the interaction and binding conformation between proteins and molecules, and promote research in the field of drug design. We will work with you to develop the most appropriate strategy and provide the most meaningful data for your research for accelerating the research of life sciences. If you are interested in our services, please do not hesitate to contact us for more information.

References

1. Stanzione F, Giangreco I, Cole J C. (2021) Use of molecular docking computational tools in drug discovery[M]//Progress in Medicinal Chemistry. Elsevier. 60: 273-343.
2. Dar A M, Mir S. (2017) Molecular docking: approaches, types, applications and basic challenges[J]. J Anal Bioanal Tech. 8(2): 1-3.

• Detection of Errors in Protein Models
• Folding and Molecular Simulation Service
• Protein Conformational Isomerism Detection and Analysis Service
• Protein Crystallization Service
• Protein Model Ranking and Analysis Service