Elbis_Bio has three strong functions added to elbis, which is convenient for protein single particle analysis with Cryo-TEM.
1. Easy Protein TEM image simulation
As you download PDB data and simulate TEM image, you can decide the best TEM optical condition to get Cryo-TEM protein image. Once you calculate protein Cryo-TEM image in a few seconds, you can check the simulated protein image changing with your mouse clicking optical values as defocus, aberration, beam intensity, and other optical conditions. Cryo-TEM image automatically changes according to the optical condition in nearly real-time.
Fig.1 Simulated images of β-galctosidase by elbis_Bio
You can choose the best optical condition with checking information limit by the figure of the CTF graph before starting actual Cryo-TEM operation. Of course, protein with ice can be simulated. You can see the effect of thickness of ice (See Fig.2).
Fig.2 Simulation for the effect of ice thickness for a TEM protein image.
Defocus=-360nm, Cs=0.002mm
Another usage is that, after modifying a protein structure, for example, adding ligand to the protein or the virus, then you can see the simulated TEM images of them within minutes. Fig.3 shows the simulated images of oxy-hemoglobin and deoxy-hemoglobin.
Fig.3 Elbis_Bio determined the optimal conditions for obtaining Cry-TEM images of deoxy- and oxy-hemoglobin.
2. Protein 3D structure evaluation
Elbis_Bio can evaluate the 3-dimensional structure of a protein which is determined by the protein single particle analysis with Cryo-TEM. First, elbis_Bio simulates TEM image from the protein’s 3D structure data and TEM optical condition. Second, elbis_Bio calculates correlation factors between real TEM images and simulated images. If the correlation factor’s values are high counts, you can be confident that the 3D structure is true. If not, it may be not reliable structure data because starting from the given structure, the simulation can’t achieve real TEM images.
Fig.4 elbis_Bio compares simulated images with actual Cryo-TEM images.