Creative BioMart provides protein-ligand docking services for the position and orientation of protein-ligand complexes (small molecules) when they bind to protein receptors or enzymes, with therapeutic applications in modern structure-based drug design. With years of protein engineering research experience, we can provide you with the best quality and most professional services. If you are interested in our services, please do not hesitate to contact us for more information.

Molecular recognition, including enzyme-substrate, drug-protein, drug-nucleic acid, protein-nucleic acid, and protein-protein interactions, plays an important role in biological processes such as signal transduction, cell regulation, and other macromolecular assemblies. Accurate prediction of binding modes between ligands and proteins is critical to understanding their interaction mechanisms and designing therapeutic interventions. Protein-ligand docking has become a particularly active area of research due to the complex and economical cost of experimental methods for determining complex structures. There are a number of interesting docking suites and algorithms that have made significant progress in predicting near-natural bonding poses by exploiting biophysical and biochemical information combined with bioinformatics. Based on the protein's structure, the researchers tried and evaluated thousands of possible binding poses, and the combination with the lowest energy score was predicted to be the best match.

Fig 1. Classification of the methods for protein-ligand docking. (Huang SY, et al., 2010)

The flexibility of proteins can increase the affinity between a given drug and its target, with a large impact on the location and orientation of binding sites. How to effectively handle the flexibility of protein receptors is one of the main challenges currently facing the field of protein-ligand docking. Creative BioMart utilizes a variety of protein-ligand docking softwares to calculate the site, geometry and energy of small molecules or peptides interacting with proteins. Our service is designed to predict and rank structures resulting from the association of a given ligand with a target protein of known 3D structure.

A protein-ligand docking program consists of two basic components, sampling and scoring. We comprehensively consider the following aspects of protein-ligand docking to accurately predict the binding mode between ligands and proteins for structure-based drug design.

(1) Protein flexibility: we adopted soft docking, side chain flexible docking, molecular relaxation docking and protein overall docking methods to account for protein flexibility.

(2) Ligand sampling: we employ shape matching, systematic search, and random algorithms to generate putative ligand orientations/conformations around protein-selected binding sites

(3) Scoring function: we employ a variety of scoring functions (such as force field, empirical, and knowledge-based scoring functions) to efficiently and reliably derive the accuracy of the algorithm.

Features of Protein-Ligand Docking

• Cvirtual screening.
• Rigid body docking and flexible docking.
• Parallel computation of efficient search algorithms for fast sampling.
• Scoring functions include hydrophobicity, van der Waals or packing interactions between aromatic amino acids, hydrogen bonding, and electrostatic forces.
• Determine the binding mode and site of ligands on proteins.
• Predict absolute binding affinities between proteins and ligands.
• Structure-based drug design.
• Multi-ligand docking with cofactors, water, and metal ionsompatible.

References

1. Huang SY, Zou X. (2010) Advances and challenges in protein-ligand docking. Int J Mol Sci. 11(8): 3016-3034.
2. Sousa SF, Fernandes PA, Ramos MJ. (2006) Protein-ligand docking: current status and future challenges. Proteins. 65(1): 15-26.

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