Creative BioMart provides protein-protein docking services to predict the structure of protein-protein complexes from the structures of individual proteins, which is of great significance for understanding a variety of biological processes and drug discovery. 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.

Protein-protein interactions play a central role in various aspects of cell structure and functional organization, and elucidation of them is critical for a better understanding of processes such as metabolic control, signal transduction, and gene regulation. Genome-wide proteomic studies will provide an ever-increasing number of interacting proteins, but using NMR and X-ray crystallography to determine the structure of protein-protein complexes is a rather tedious and tedious process. Therefore, it is important to develop docking methods that can elucidate the details of specific interactions at the atomic level, predicting complex three-dimensional structures based on their known compositions. Over the years, many methods of protein-protein molecular docking have been developed at home and abroad.

Fig 1. Flowchart for protein-protein docking. ( Zhang Q, et al., 2016)

Predicting the structure of protein-protein complexes is a difficult problem, and major challenges include identifying the right solution, and properly handling flexibility and conformational changes. Creative BioMart utilizes a variety of docking softwares to perform a thorough search of the entire conformational space of the two proteins, allowing fast and accurate docking of protein complexes based on biochemical or biophysical information, resulting in stable complex formation.

Protein-protein docking mainly consists of the following two stages:

(1) Sampling: sampling is used to generate many plausible protein-protein binding conformations. Our procedure based on the Fast Fourier Transform (FFT) geometric identification algorithm, the geometric hashing algorithm and the Monte Carlo search algorithm starts with a global search and evaluates the energies of billions of docked conformations on a grid.

(2) Scoring: scoring can sort all these conformations. Scoring functions (including re-ranking and ranking methods) are based on force fields and knowledge-based scoring functions.

Features of Protein-Protein Docking

• Scoring functions considering shape complementarity, electrostatics, desolvation.
• Exhaustive search of the entire conformation space to ensure accuracy.
• Clustering of low-energy docked conformations.
• High-resolution flexible docking for complex structural refinement.
• Identification of hotspot residues in protein-protein interactions.
• Membrane protein docking.
• Adding flexibility to docking.
• Handling protein folding and structure prediction in the context of docking.

Reference

1. Zhang Q, Feng T, et al.. (2016) Recent Advances in Protein-Protein Docking. Curr Drug Targets. 17(14):1586-1594.

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