Flexible docking means that the conformation of the research system can basically be changed freely during the docking process. Generally used to accurately consider the recognition between molecules. Now, CD ComputaBio offers flexible peptide docking service to meet the specific needs of different customers.
First, a sequence-based skeleton image collection is generated, and the Monte Carlo sampling and coarse-grained model are used to quickly simulate the "folding" process of the polypeptide near the binding pocket, and then under the all-atom model, the skeleton structure and side chain arrangement are explicitly optimized. The biggest advantage of this method is that it is not sensitive to the initial input conformation and does not need to predict the specific conformation of the polypeptide. The user only needs to place the polypeptide near the possible binding pocket.
1. Defines the initial complex conformation
2. Generate short peptide fragments
3. The generation of the skeleton structure is divided into two stages:
Coarse-graining stage: Through simulated annealing, fragment insertion based on fragments, and translation and rotation between rigid bodies, a large number of bone structure image sampling is performed to simulate the conformational changes of local polypeptides. These three disturbance methods have their own trigger probabilities.
Optimization stage: After a small amplitude dihedral angle perturbation sampling (shear & small mover) is performed on the skeleton, the energy between the rigid bodies is minimized, and the arrangement of the side chain Rotamer is calculated. In this stage, the weights of the attractive and repulsive potentials of van der Waals forces are continuously adjusted until they return to the default values.
|Project name||Flexible peptide docking|
|Our services||CD ComputaBio offers flexible peptide docking service to meet the specific needs of different customers.|
|Timeline||Decide according to your needs.|
|Deliverable||We provide you with raw data and analysis service.|
CD ComputaBio provides professional and flexible peptide docking services to meet the specific needs of old customers on time and on budget. CD ComputaBio relies on world-class technical expertise, we provide customers with the best quality one-stop flexible peptide docking service, including the development of solutions according to different scientific research needs. Please feel free to contact us for more detailed information, our scientists will tailor the most reasonable plan for your project. If you want to know more service prices or technical details, please feel free to contact us.