Comments (3)
Hi Amin,
Sorry for the very late response!
I'm sorry for the bad documentation concerning point mutations. This is currently a work in progress, but in the future it should be possible to mutate peptides with transformato as long as they have the same overall charge!! (Mutating a positive charged amino acid to a negative will not be possible at this stage)
The final idea would be to be able to handle point mutations exactly like relative binding free energies. Currently, there is no support for amber, but I am working on that as well. If there is support, it would be sufficient if you have a parm7 and rst file.
from transformato.
Thanks @JohannesKarwou for your response.
I look forward to these developments.
Most of the mutations I am interested in conserve overall charge.
Many of them include changing just one hydrogen with a methyl or a halogen group.
I have experimental affinity data for these substitutions which I can correlate the theoretical results with.
If you have a pre-release version at some point, I would be more than happy to run tests and report the results.
Best,
Amin.
from transformato.
That sounds like a great use case!
I will let you know if we have something more robust so you can test it!
from transformato.
Related Issues (12)
- Possibility of multiple restraints acting on single atom for automatic restraints. HOT 1
- mutate torsions HOT 1
- Alternate system inputs HOT 1
- Hydrogen Mass Repartitioning
- documentation HOT 3
- More ions HOT 1
- Charge compensation between intermediate states
- TODO for point mutations HOT 1
- changing to new openmm version
- Representation issue in README.md HOT 2
- problems with pymbar version 4 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 transformato.