Comments (4)
from proteinmpnn.
Did you try fast relax of the WT and the design? Were there any clashes? How did you do the threading?
…
On Wed, Aug 3, 2022 at 12:24 AM 18217265596 @.> wrote: hi proteinmpnn team i read the paper about the function design part i wonder if protein mpnn can be used to design ppi in certain interface i tried it with one side of the interface with residue within 5A of the other side into design and other fixed the designed sequences are predicted of their structure and docked to the other side but ddG calculated by interface anaylzer with beta nove 16 is positve but wt is much negative is there anything to discuss about such situation? — Reply to this email directly, view it on GitHub <#15>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZDHRAASB6NSJ5R5OG5QFTVXHYBJANCNFSM55NLUB7A . You are receiving this because you are subscribed to this thread.Message ID: @.>
I did not fast relax WT , but WT crystal structure was used in flexddg in designing interface residues and computational results were fine. no clashes in wt anyway
and sorry i dont understand what means "do the threading" can you explain it a little?
in proteinempnn i just used the scripts Example from vanilla_proteinmpnn/examples/ to design some complexes
and changed the residue number to my interface and the other side of the interface fixed
from proteinmpnn.
Did you try fast relax of the WT and the design? Were there any clashes? How did you do the threading?
…
On Wed, Aug 3, 2022 at 12:24 AM 18217265596 @.> wrote: hi proteinmpnn team i read the paper about the function design part i wonder if protein mpnn can be used to design ppi in certain interface i tried it with one side of the interface with residue within 5A of the other side into design and other fixed the designed sequences are predicted of their structure and docked to the other side but ddG calculated by interface anaylzer with beta nove 16 is positve but wt is much negative is there anything to discuss about such situation? — Reply to this email directly, view it on GitHub <#15>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZDHRAASB6NSJ5R5OG5QFTVXHYBJANCNFSM55NLUB7A . You are receiving this because you are subscribed to this thread.Message ID: @.>
also im not sure if im doing it the right way to use the proteinmpnn designed sequence to predict structure in colabfold and align to wt to calculate interface ddg, since proteinmpnn has no structure output or is such calculation just wast of time before experiment of the designed sequence?
from proteinmpnn.
You will need to optimize (relax with BB and maybe with side-chain restraints) AF2-predicted structures, they are in a different force-field than X-ray structures, so Rosetta scores will always be very positive for them. Even better, just get the X-ray structure and thread the newly designed sequences onto them (you can do this with flexddG), and then score.
from proteinmpnn.
Related Issues (20)
- Questions about model weights
- .Fa Output reorganization question
- Sampling temperature for flexible chains
- what pdbx package does parse_cif_noX.py expect? HOT 1
- Global_score
- No use of GPU?
- `parse_cif_noX.py` misses some chains in CATH? HOT 2
- Training model
- Retrieve per-position scores or score a chain in the context of another
- whether to redesign low confidence aas
- Design complexes with unknown chains (proposed fix included)
- Amino acid sequence has too many "K/E" HOT 2
- How do I use a PSSM with proteinMPNN?
- Need of assistance and advising
- Model is adding an amino acid to the original sequence HOT 5
- Creates hydrophobic surface patches wit many Ala side chains HOT 2
- Training time HOT 1
- What is the difference between --conditional_probs_only_backbone and --unconditional_probs_only HOT 1
- Empty parsed_pdbs.jsonl file from parse_multiple_chains.py helper script? HOT 1
- RuntimeError: Class values must be smaller than num_classes. | protein_mpnn_utils.py & mask_size issue?
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 proteinmpnn.