GithubHelp home page GithubHelp logo

Abnormal results about proteinmpnn HOT 5 CLOSED

zdf1122 avatar zdf1122 commented on July 19, 2024
Abnormal results

from proteinmpnn.

Comments (5)

dauparas avatar dauparas commented on July 19, 2024

hello! does the top sequence in the .fasta output file also have those Xs? Could it be that your PDB file has residue jumps in those places?

from proteinmpnn.

zdf1122 avatar zdf1122 commented on July 19, 2024

hello! does the top sequence in the .fasta output file also have those Xs? Could it be that your PDB file has residue jumps in those places?
thank you very much !

from proteinmpnn.

zdf1122 avatar zdf1122 commented on July 19, 2024

hello! does the top sequence in the .fasta output file also have those Xs? Could it be that your PDB file has residue jumps in those places?

Sorry to bother you again. I wonder if whether the higher the score, global_score and seq_recovery, the better the result.
image

from proteinmpnn.

dauparas avatar dauparas commented on July 19, 2024

Lower score is better; the score (negative log probability) represents model's uncertainty about the predictions.

from proteinmpnn.

tony-res avatar tony-res commented on July 19, 2024

I've got a similar output. From what I can tell the original PDB did have residue jumps that were labeled as "-" in pyMol and appear to come out as "X" in the ProteinMPNN output.

If I wanted to put this sequence into something like AlphaFold or ESM, then would I simply remove the "X"s? Or is there more to it?

e.g. "SEQVXXXKIXM" becomes "SEQVKIM"

from proteinmpnn.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.