Academic communication record for predicting protein interaction software

A: I would like to ask what is the method for predicting the interaction between two proteins?

Yin Fu Technology: Protein-protein docking method. Protein-protein docking can be done with a lot of software, such as ZDOCK (which is also integrated in Discovery Studio), Hex, and Rosetta. Our platform will also be available in the future.

B: Excuse me, how do you charge for molecular docking?

Yin Fu Technology: The platform molecule acceptance fee standard is here: http://

C: I would also like to ask if there is a corresponding method and software for predicting the interaction between proteins. How to charge?

Yin Fu Technology: ZDOCK is free, Rosetta can apply for academic license.

D: Can you ask if vina can do protein docking?

E: Yes.

F: The effect is not good.

Yin Fu Technology: Generally do not use vina for protein-protein docking. An alternative is to use ZDOCK for rigid docking and then calculate molecular dynamics.

D: ZDOCK docking effect is not good. After adding the binding site limit in the early stage, the spatial position after docking is still deviated.

Yin Fu Technology: Then use Rosetta. I don't know if you have any other recommendations.

G: I personally feel that zdock is very accurate.

Yin Fu Technology: That's good. I am planning to develop these software into a convenient solution.

H: That Rosseta is particularly troublesome, and I have learned a lot of pits since I learned. I don't know if anyone has good information or exchange groups.

Yin Fu Technology: Rosetta's official tutorial is very good: https://#preparing-structures-for-docking

H: That pyrosetta (Python package) gives too many functions. There are quite a few pits to master.

Yin Fu Technology: Protein-protein docking can also be used with I-TASSER: https://zhanglab.ccmb.med.umich.edu/services/.

H:rosetta can design proteins. Should this be more technical than docking and MD? Rosetta is good at designing proteins. If you are aiming at this goal, it is recommended.

Yin Fu Technology: Research Rosetta, to write a tutorial or experience sharing, welcome everyone to contribute!

A: Can these software win systems be used?

Yin Fu Technology: There should be win, http://zdock.umassmed.edu/.

A: If you just want to predict whether the two proteins interact, what better website or something?

Yin Fu Technology: Try this http://string-db.org/.

H: Is the cloud platform your own server or based on Alibaba Cloud?

Yin Fu Technology: Our own server.

I: Can you use your platform for free docking?

Yin Fu Technology: There are 2 calculation coupons for registration now.

H: Is there a template report result? I can show you what indicators or results the platform can make.

Yin Fu Technology: There is a public article. Because there are so many things at hand, many functions are still being developed, and there is no time to do templates. It will be gradually improved in the future.

At present, our platform has two programs, vina and dock6, which can be used for docking proteins, nucleic acids, peptides and small molecules, except for protein-protein. When a polypeptide or a nucleic acid is used as a ligand, it supports only less than 6 amino acids and bases, and is treated as an organic small molecule. Because the quantity is too much, it is not accurate.

H: I have always been interested in molecular docking and MD. I have searched for such micro-signals. Only you have always insisted on sharing articles specifically for these.

Wavelength of ECD experimental data

Yin Fu Technology: I would like to ask friends in the field of natural products. In the ECD experimental data measured by each instrument, the wavelengths are all integers. Is there a decimal number? I have not operated the instrument, so it is not clear.

J: It should be configurable. I remember that there is a parameter that sets the number of data points measured per second.

We are currently measuring integers, and the parameters are the ones used.

I currently have no decimals, only integers, I don't know if there will be any parameters after tuning.

Yin Fu Technology: I think most people should not be set to have decimals, otherwise the data points will be ten times larger.

J: But the data I calculated is all with decimals. I have to filter and keep the integers.

Schrödinger Tutorial

K: Is there a tutorial for Schrödinger or the new version of ds?

Yin Fu Technology: These softwares come with their own tutorials.

K: That help looks a bit messy.

Yin Fu Technology: Online search should be there to see if other group friends have any information to share.

K: Sometimes the parameters of those settings don't know if you want to follow the tutorial.

Yin Fu Technology: This requires you to have enough knowledge of the parameters.

K: It still seems to look at the introduction in help.

Yin Fu Technology: Yes, it is beneficial to open the book.

For more information, please visit or follow the WeChat public account "Yin Fu Technology". Our company has established the WeChat academic exchange group to build an interactive platform for communication and communication among friends in the biomedical field. If you want to join a group of friends, please enter "Add Group" in the WeChat public account menu bar and follow the prompts.