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Side Chain Modeling of Antibody

Creative Biolabs has successfully built several antibody structure models. With experienced scientists hammering at Creative Biolabs, we are confident in providing best in class side chain modeling service to contribute greatly to the success of your projects.

Side Chain Conformation Prediction of Antibody

Antibody side chain conformation prediction is an essential step in both antibody design and antibody structure modeling. In the past years, many efforts have been dedicated to the prediction of protein side chain conformations, resulting in the progress of many side chain packing programs. However, under the existing search algorithms and current computational power, a thorough search via the continuous side-chain conformations is inefficient and infeasible. Fortunately, side-chain dihedral angles are not averagely distributed, they occur in tight clusters around certain values. On account of these clusters, the side-chain conformational space enables to be discretized into rotamers which stand for the conformations of these clusters. And an ensemble of rotamers for all side-chain types is called a rotamer library. According to the rotamer definition, side-chain modeling enables to be effectually transformed into a combinatorial search problem, which is to determine the best rotamer combination from all possible combinations of side-chain rotamers. As to this methodology, many efforts have attempted, such as development of powerful scoring functions, well-sampled rotamer libraries, and effective search methods.

Side Chain Modeling of Antibody

CIS-RR Method

In order to perform a more effective side-chain modeling, Creative Biolabs combines the advances from side-chain modeling in both rotamer-based search and rotamer optimization. Our approach, named CIS-RR, allows clash-detection guided iterative search (CIS) of side-chain rotamers while continuously optimizes side-chain conformations through a conjugate gradients approach. Compared to typical iterative search approach, careful implementation of CIS-RR displays remarkable advancement of prediction accuracy and elimination of atomic clashes. Moreover, benchmark testing exhibits that CIS-RR removes atomic clashes much more powerful and enables better prediction accuracy while having comparable computational cost, compared to existing side-chain modeling programs.

RASP Method

The RASP, refers to Rapid Side-chain Predictor, which construct the protein side chains over one order of magnitude more rapid than the best existing ones while performing comparable accuracy. RASP takes advantage of clash detection-guided side chain optimization to assuage atomic clashes induced by rigid rotamer approximation. However, different form CIS-RR, RASP efficiently eliminates atomic clashes after the formation of a high-quality structure. Hence, in RASP, we mainly concern the quick production of high-quality initial structures and rapid remove of atomic clashes by relaxing those residues in clashes.

With our high-quality side chain modeling service, the experienced scientists here at Creative Biolabs are dedicated to helping you develop antibody structure models. We also provide other various services regarding antibody structure models. Please feel free to contact us for more information and a detailed quote.

References

  1. Cao, Y., (2010). “Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.” Bioinformatics, 27(6), 785-790.
  2. Miao, Z., (2011). “RASP: rapid modeling of protein side chain conformations.” Bioinformatics, 27(22), 3117-3122.

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