Comments (7)
yangkky
commented on May 22, 2024
Yes, they are the standard definitions. We use the same method for
calculating them from structure as Ingraham. Thanks for pointing out that
the figure is wrong: I'll work on fixing that.
…On Sat, Jun 25, 2022, 4:50 AM Wenhao-Jin ***@***.***> wrote:
Hi authors, I am trying to use your MIF-ST model and now preparing the
node/edge features. Just to be sure I got the features correctly, I was
wondering if the omega, theta and phi angles in your paper are referring to
the torsion angles that are used in peptide/protein structure (definitions
can be found here <https://swissmodel.expasy.org/course/text/chapter1.htm>
).
According to Figure 2 in your MIF paper
<https://www.biorxiv.org/content/10.1101/2022.05.25.493516v1.full.pdf>,
the answer is no. But the Figure 2 was a bit confusing to me since the
omega, theta and phi are all related to the beta carbons. However, not all
of the amino acids have beta carbons. I also checked the paper from
Ingraham et al. (2019) which is cited in your MIF paper for this part. In
that paper they didn't give much details but used the terms "omega", "psi"
and "phi". Could you help me with this? Great thanks in advance!
—
Reply to this email directly, view it on GitHub
<#7>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ADEMNWB6M7C6MWMOFDCKY3LVQ3B67ANCNFSM5ZZ6LKHA>
.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
from protein-sequence-models.
Wenhao-Jin
commented on May 22, 2024
Got you. Thanks for clarifying it, @yangkky!
from protein-sequence-models.
hyeh20
commented on May 22, 2024
@Wenhao-Jin Just wanted to clarify on this - the angle features used follows the angles described by the trRosetta paper and unconventional compared to how dihedral angles for proteins are typically defined.
from protein-sequence-models.
Wenhao-Jin
commented on May 22, 2024
@hyeh20 Thank you so much for the clarification! Just to make sure, for the dist value, I was also wondering if MIF also used the distance between beta carbons as trRosetta did. Besides, is there some script or package available for generating these angles. Thanks so much again!
from protein-sequence-models.
hyeh20
commented on May 22, 2024
Yes, the distance should be between beta carbons, we will update our figure in our next revision.
For scripts on how to generate these angles: If you are starting with a pdb file for your proteins, please use the functions in pdb_utils.py. parse_PDB will generate a coordinates dictionary and then you can use process_coords to generate the angle features. These scripts were directly modified from the trRosetta paper.
from protein-sequence-models.
yangkky
commented on May 22, 2024
@Wenhao-Jin sorry for the confusion: @hyeh20 is correct.
The parsing functions are here: https://github.com/microsoft/protein-sequence-models/blob/main/sequence_models/pdb_utils.py
from protein-sequence-models.
Wenhao-Jin
commented on May 22, 2024
Thanks so much for the help! Sorry for the delayed response, it works on my side. Really appreciate it!
from protein-sequence-models.
Related Issues (16)
- Old Zenodo link in readme HOT 1
- No such file or directory: 'examples/results/some_proteins_mifst/wt_mifst_mean.pt' HOT 1
- zero-shot inference and inverse folding with fixed residues HOT 2
- This DOI prefix is currently inactive. HOT 4
- Weights for MIF-ST and MIF-GVP HOT 3
- Could you public the training code of MIF? HOT 1
- Confusing results taken from FLIP paper HOT 1
- TrRosetta example doesn't work
- extract_mif.py Tensor Size runtime error HOT 4
- calculate stability and melting temperature from protein sequence HOT 5
- Is the theta angle here the same as the Psi angle in the dihedral angle?
- Applying BiGCARP to other genomes
- This repo is missing important files
- requirements.txt is empty
- DDP with sampler HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
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.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from protein-sequence-models.