Metadata-Version: 2.1
Name: sbmlcore
Version: 0.1.2
Summary: Constructs core features table for the application to machine learning models
Home-page: https://github.com/fowler-lab/sbmlcore
Author: Philip W Fowler and Charlotte I Lynch and Dylan Adlard
Author-email: philip.fowler@ndm.ox.ac.uk
License: MIT
Project-URL: Documentation, https://github.com/fowler-lab/sbmlcore
Project-URL: CI, https://github.com/fowler-lab/sbmlcore/actions
Project-URL: Source, https://github.com/fowler-lab/sbmlcore
Project-URL: Tracker, https://github.com/fowler-lab/sbmlcore/issues
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

# sbml-core
Collection of core classes and functions for structure-based machine learning to predict antimicrobial resistance.

This is a pre-release alpha version - it may not be fully functional for your requirements and it is also subject to change with no notice!

See notebooks walkthrough.ipynb and addition_methods_walkthrough.ipynb for
quick user tutorials.

## Included features

### Changes in Amino Acid Properties

- Volume
- Hydropathy scales: Kyte-Doolittle ([paper](https://www.sciencedirect.com/science/article/abs/pii/0022283682905150?via%3Dihub)) and WimleyWhite ([paper](https://www.nature.com/articles/nsb1096-842))
- Molecular weight
- Isoelectric point

### Secondary structure

- STRIDE ([website](http://webclu.bio.wzw.tum.de/stride/) and [paper](https://onlinelibrary.wiley.com/doi/10.1002/prot.340230412))

### Solvent accessible surface areas

- FreeSASA ([paper](https://f1000research.com/articles/5-189/v1))
- STRIDE ([website](http://webclu.bio.wzw.tum.de/stride/) and [paper](https://onlinelibrary.wiley.com/doi/10.1002/prot.340230412))

### Likelihood of changes in protein function

- SNAP2 ([server](https://www.rostlab.org/services/snap/) and [paper](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S1))

### Effect of mutation on protein stability

- DeepDDG: a more recent neural network that claims to outperform DUET, PopMusic etc. ([paper](https://pubs.acs.org/doi/10.1021/acs.jcim.8b00697) and  [server](http://protein.org.cn/ddg.html)). Can do all possible mutations in one job.

### Structural distances

- Distances between mutated residues and any atom/group of atoms of interest. Uses MDAnalysis ([paper1](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144279/) and [paper2](https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html)).

## To potentially include at a later stage
 - Secondary structure: DSSP (do not anticipate much difference to STRIDE)
 - Protein stability:
    1. StabilityPredict. Online metapredictor, single amino acid at a time. Josh used in the pncA paper but had to contact them directly to run the entirity of PncA. ([paper](https://www.jbc.org/article/S0021-9258(20)34176-4/fulltext))
    2. DynaMUT. Also claims to outperform DUET etc. ([paper](https://academic.oup.com/nar/article/46/W1/W350/4990022)). Can process a list of specified mutations in one job. ([server](http://biosig.unimelb.edu.au/dynamut/))
