De Novo Modeling Service

As a novel protein structure prediction method, de novo modeling is mainly used for three-dimensional (3D) structure construction of smaller proteins by computational algorithms and analysis. Creative Biolabs offers high-quality de novo protein structure modeling services to global customers. Our professional services have assisted a lot of customers to overcome multiple challenges in structure prediction.

Background of De Novo Modeling

During the past decades, the total number of discovered proteins has almost kept exponential growth, especially the number of protein sequences increases dramatically owing to the development of DNA sequencing technology. The various advanced protein structure prediction technologies have thrived in recent years because the conventional major experimental techniques, such as X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy, can no longer meet the current needs of protein structure determination. De novo modeling is one of the newly-developed computational techniques for protein structure prediction.

De novo modeling is an algorithmic process to predict protein tertiary structure from its amino acid sequence, which is much more computationally intensive than comparative modeling. Generally, de novo modeling is limited to relatively small protein sequences (<100-150 residues) due to massive computational resources and conformational space. Different to commonly used template-based modeling, de novo modeling is advantageous when no template is recognized and is necessary for non-homologous loop regions construction. Despite computational difficulties and smaller protein limitation, de novo modeling-based protein structure prediction has made achievements in the application for protein engineering and drug design.

Fig.1 Computational workflows for cross-link guided molecular modeling centered on ROSETTA protocols and Xwalk software. (Kahraman, 2013)

Services

De novo modeling is a computational algorithms-dependent protein structure prediction approach with a multitude of methodologies and techniques, such as Rosetta, NiDelta, UniCon3D, etc. Firstly, de novo protein structure modeling tends to produce a series of possible candidate structures (called ‘decoys’) guided by scoring functions and sequence-dependent biases. Then, we can select the most native-like conformations from these candidates using scoring functions and choose the conformation with the global minimum folding energy.

Armed with the first-class technological platform, Creative Biolabs provides protein structure prediction services by computational de novo modeling method. Once the primary sequence of your interested protein is determined, we can give you candidate conformations by our computation algorithms system. Followed by, native-like structures are provided using physics-based functions or knowledge-based functions. High-resolution optimization is also available to fine-tune the final native-like structures.

Features

Multiple methodologies and algorithms
Experienced scientists proficient in protein engineering
High-quality and reproducible results with competitive prices and on-time delivery

Creative Biolabs has proudly developed the advanced protein engineering platform to provide comprehensive protein services to our valued customers. We are confident in offering protein structure prediction services by the de novo modeling approach based on accumulated experience.

You can directly contact us and communicate your specific demands with us for more information.

Reference

Kahraman, A.; et al. Cross-link guided molecular modeling with ROSETTA. PLoS One. 2013, 8(9): e73411.

All listed services and products are For Research Use Only. Do Not use in any diagnostic or therapeutic applications.

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