A: The novice wants to ask, how does the docking result judge the combination of small molecules and proteins, forming a hydrophobic bond or a hydrogen bond?
B: The lower the score, the better. Generally, a known ligand is set for reference, or it is used to check whether the parameters are reasonable.
A: I chose a protein with a ligand, and after doing the docking with the protein and the molecule, I got this result.
B: As long as the score of this ligand is lower, it is definitely more likely to be there!
E: The novice wants to ask, how to determine the position and coordinates of the docking box when the ligand and protein are docked?
D: Check the ligand.
B: According to the previous literature research, it is necessary to generally know the location of the binding site. Otherwise you have to do a global docking.
E: Is the original document of the protein of pdb downloaded? The overall docking feels wrong.
D: You have to know the union and the pocket first.
B: Not necessarily, for example, some mutation studies will tell you about the general binding site.
D: Binding pockets can be located with amino acid residues.
(Hint: See "How to determine the interface bag?" for more dry goods)
F: I have a problem. It is known that the ligand binding energy-9, my bunch of ligand binding energy is -2 to -4, is it meaningful? The binding position is consistent.
Yin Fu Technology: Vina docking? More than -4 basically does not make sense.
F: It is autodock. I am a mixture of peptides. I have identified the ingredients and then docked them as ligands. They are basically -2~-4. Basically it doesn't make sense?
Yin Fu Technology: It is not reliable to see the value. Is it true that the combined mode is normal?
F: How do you think about the combination mode? What parameters are you looking at?
Yin Fu Technology: You can compare the original ligands to see if your ligands are combined in the corresponding pockets, whether they are fully integrated in the inside, or whether a large part is exposed to the solvent (considering the poor score, combined mode) It should not be too good).
You are docking the peptide, the molecular weight should not be small, the light hydrophobic effect will not make the score so bad, so I suspect that there is a problem with the combined conformation.
B: A molecular dynamics simulation can be added later.
F: I am the structure of the painting on chemdraw and the energy is minimized, and then processed on the ADT. When the torsion is selected, the rotatable key in the display structure is greater than 32. I will adjust it to 32 or less. I don't know if this is correct.
Yin Fu Technology: Polypeptide is a peptide, at least it has 5, 6 peptides.
F: From hexapeptide to decapeptide. Well, basically it is 7,8.
Yin Fu Technology: I said earlier in the group that our platform has the function of peptide docking, but it is limited to 6 peptides, which means that too many rotatable keys will cause incomplete docking.
F: Yes, what should I do in this situation?
Yin Fu Technology: So, you'd better use the software that specializes in peptide docking to do this topic.
F: I see that the literature has almost the same thing as I did. They also use autodock, hey, kill me. I have too many peptides, more than 20.
Yin Fu Technology: The literature is not necessarily correct and must be skeptical. Try this online service: http://biocomp.chem.uw.edu.pl/CABSdock/
F: That is still a top publication, thank you for your answer.
Yin Fu Technology: Not necessarily, look at the field, see what role the docking is, if it is just a foil, it may not be done well.
H: Is there a comprehensive platform for predicting compound activity?
Yin Fu Technology: Compound activity prediction, calculation is a virtual screening, such as the use of molecular docking methods. What is more comprehensive, compound library, or software method is complete, or other?
H: It means that for an unknown compound, it can be reversed to find a protein with better binding, and then predict the action of the compound.
Yin Fu Technology: Yes, @墨çµæ ¼ has this business. Teacher Xu’s team also has an online service: http://
Ingelinger: Thanks, machine learning-based method target prediction (database ChEMBL24 version, naive Bayesian multi-class prediction target): http://targetfishing.molcalx.com.cn/ml.html, containing more than 1900 targets, Give the probability.
Ingelinger: Target prediction for some typical diseases (based on molecular shape): http://targetfishing.molcalx.com.cn.
H: Thank you, can you recommend a few more similar ones?
Yin Fu Technology: Others I don't understand. Foreign research groups should also have it, search on Google or bing.
J: I also have small molecular products that are broken down on hand. I also want to do research related to diseases. @墨çµæ ¼ I want to associate my small molecule drug with a disease. How can I predict?
Ingelinger: You can try it directly, you know, the structure is just fine.
J: Yes. After the prediction is over, experiment with it.
Ingelinger: Before being verified, it is a prediction, not counting. Forecasting is just a hint, there are a lot of things to be further ruled out: just suggest that you can pay attention to this target, and then exclude the impossible according to your own knowledge.
K: Excuse me, why is there a lot of pdb code for a target? How should I choose it?
L: high resolution (editor press: the smaller the resolution, the higher the resolution, the best is less than 2), there is a ligand.
K: Is the protein inside the same one? I looked at the sequence and it seems to be different. Thank you, I have not noticed the resolution before, thank you for your reminder. L: If you are doing people, choose people.
H: Take a look at uniprot.
I: Integration (Editor's note: Ensemble, some translations are "association") Docking (scoring) is a very general strategy, much more accurate than traditional methods. Integration strategies have been around for many years, so check out the overview: Amaro, RE; Baudry, J.; Chodera, J.; Demir, Ö.; McCammon, JA; Miao, Y.; Smith, JC Ensemble Docking in Drug Discovery. Biophys J. 2018, 114 (10), 2271–2278. https://doi.org/10.1016/j.bpj.2018.02.038.
K: @I Hello, what software can I use to integrate the strategy? Is it a big help for drug design? I: Integrated docking is a strategy, you don't need special software, of course, some software is customized for this strategy. .
K: Ok, let me see the review. I have never heard of this strategy before. I: Molecular docking was originally used for early detection, which improved the hit rate and accuracy, and of course helped.
A: How do you look at the original ligand score? As a result, only a few of my small molecules scored with a ligand dock?
Yin Fu Technology: Yes! It can also be scored or not, or in-situ minimization. The scheme on the Yin Fu cloud platform has multiple computing modes.
A: I don't seem to have the ability to score only.
Yin Fu Technology: Are you using our platform?
A: No, use moe.
Yin Fu Technology: MOE does not seem to have this function, search for keywords in its help to see: in situ, in-situ, docking and then score, can test whether the software has the ability to predict correctly.
C: I would like to ask if the molecular value of the compound library is more than 100% when using the pharmacophore ligand profile to screen the compound library.
D: 4 points or more.
G: The top seven compounds after Vina, I optimized the charge of the protein and the small molecule. There should be no shortage of non-polar hydrogen and N-state. After the cdocker, only one small molecule is docked, then I How should we reasonably explain this phenomenon? According to the Vina protocol, VS hits must be bound to the active area, and the cdocker hits a compound. Are other VS hit compounds too large to fit into the active pocket of the cdocker docking?
Yin Fu Technology: (Molecular is too big) is possible. Use software to open the vina docking results to see the molecular binding. Try to increase the pocket range of the CDOCKER. You can also try other docking methods, such as Dock6.
C: Will the downloaded pdb protein, such as 4bkx, show that the ligand is an acetate molecule, and how does the docking treatment protein define the active site? Is the acetic acid selected or one of the active sites of the protein?
G: Look at the relevant literature.
M: Select the ligand, then select from current ... to generate the active sphere, the radius å•¥ can be adjusted.
C: This is done by finding that the protein and ligand docking results are not very good.
M: It is possible to try to extract protein receptors from other crystal structures containing this protein for docking.
(Hint: In general, the acetate molecule is not a ligand, just a solvent or a co-solvent; the method of defining the active site/pocket can refer to "How to determine the interface bag?")
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