Protein modeling is a strong competency at Creative Biolabs. We offer in silico protein modeling service to predict the secondary and tertiary structures of target proteins. Our professional team has extensive experience in conformational prediction, protein modeling, and protein properties mining. Our protein modeling tools are full scope and high interoperability, which make us superior to other competitors in the field.
The concept of “sequence implies the structure and structure implies the function” shows that the importance of protein structures for protein functions. The biological function of a protein is totally dependent on its native 3D structure. Generally, macromolecular structures are determined by X-ray crystallography and NMR. However, some proteins are too large to NMR analysis and cannot be crystallized for X-ray crystallography as well. The emerging of novel sequencing technologies along with the introduction of various informatics tools provides a faster and efficient manner for sequencing proteins and building protein models.
Creative Biolabs uses three different methods for predicting the 3D structures of proteins:
Figure 1. Three-dimensional structure of proteins.
Homology modeling
Among the three major approaches for predicting 3D structures, homology modeling is the easiest one. Homology modeling, also designated as comparative modeling, is based on the observation that structure evolution is more stable than associated sequence evolution, so that similar sequences adopt practically identical structures, and distantly related sequences still fold into similar structures. Therefore, the available information of ≥50% homologous protein sequence is collected and compared to target proteins for constructing structures.
Protein threading
Another protein modeling method we provide named protein threading or fold recognition. It is used for those proteins which do not have homologous protein structures in the Protein Data Bank (PDB), FSSP, SCOP or CATH. This method is based on the observation that the number of different folds in nature is fairly small, and even proteins of very different sequences can have the same folds. Creative Biolabs finds the best-fit template for your proteins and use fold recognition tools to generate structure models.
Ab initio methods
Ab initio quantum chemistry methods are used in the circumstance that your protein neither has homologous structures nor suitable templates. Thermodynamic and molecular energy parameters are used to propose a 3D conformation of entire protein with minimum entropy and maximum stability.
The accuracy of protein modeling depends heavily on the sequence identity between target and templates. If your protein sequence and the template have identity above 50%, we ensure reliable models, with only limited errors in the side chain and loops position by homology modeling. The accuracy is comparable to the structure solved by NMR.
For more detailed information, please feel free to contact us or directly sent us an inquiry.
Reference
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