| Name | ipsae JSON |
| Version |
1.0.0
JSON |
| download |
| home_page | None |
| Summary | Calculate ipSAE scores for protein-protein interactions in AlphaFold2 and AlphaFold3 models |
| upload_time | 2025-09-15 18:11:53 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | MIT |
| keywords |
protein
alphafold
bioinformatics
structural-biology
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# ipSAE: for binders screening
## Installation
```bash
pip install ipsae
```
## Usage
Run `ipSAE` tool from the command line terminal in Linux. It takes the Alphafold2, Alphold3 and Boltz2 multimers PAE file in .json and .pdb or .cif file format as input, and distance cutoff values.
### Command-line Help
```
$ ipsae --help
```
```
ipSAE
Scoring function for interprotein interactions
-------------------------------------------------
Version: 1.0
Author: Samee Ullah
Email: sameeullah@bs.qau.edu.pk
LinkedIn: https://www.linkedin.com/in/ullah-samee/
-------------------------------------------------
Based on the original work of Roland Dunbrack.
usage: ipsae [-h] pae_file structure_file [cutoffs ...]
Calculate ipSAE scores for protein-protein interactions
positional arguments:
pae_file PAE file (JSON or NPZ)
structure_file Structure file (PDB or CIF)
cutoffs Optional: PAE and distance cutoff values. Defaults are 15
for AF2 and 10 for AF3/Boltz1.
options:
-h, --help show this help message and exit
Examples:
For AlphaFold2:
ipsae alphafold2_multimer.json alphafold2_model.pdb 15 15
For AlphaFold3:
ipsae full_data_0.json model_0.cif 10 10
For Boltz:
ipsae pae_model_0.npz Boltz_model.cif 10 10
```
### Examples
#### AlphaFold2
```bash
ipsae scores.json model.pdb 15 15
```
default distance cutoffs of 15.
#### AlphaFold3
```bash
ipsae full_data_0.json model_0.cif 10 10
```
default distance cutoffs of 10.
#### Boltz1
```bash
ipsae pae_model_0.npz model_0.cif 10 10
```
default distance cutoffs of 10.
## Output Files
The tool generates three output files:
1. **`<name>_<pae>_<dist>.txt`**: The main output file with chain-chain scores.
2. **`<name>_<pae>_<dist>_byres.txt`**: By-residue scores.
3. **`<name>_<pae>_<dist>.pml`**: A PyMOL script for visualizing the ipSAE scores.
### Main Output File Format
The main output file contains a table with the following columns:
| Chn1 | Chn2 | PAE | Dist | Type | ipSAE | ipSAE_d0chn | ipSAE_d0dom | ipTM_af | ipTM_d0chn | pDockQ | pDockQ2 | LIS | n0res | n0chn | n0dom | d0res | d0chn | d0dom | nres1 | nres2 | dist1 | dist2 | Model |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
## Credits
This tool is based on the original work of Roland Dunbrack.
Raw data
{
"_id": null,
"home_page": null,
"name": "ipsae",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": null,
"keywords": "protein, alphafold, bioinformatics, structural-biology",
"author": null,
"author_email": "SameeUllah <sameeullah@bs.qau.edu.pk>",
"download_url": "https://files.pythonhosted.org/packages/60/43/b0061882bfa43fa540050970271be297a27f97eec2e4984f4dfc6c75178b/ipsae-1.0.0.tar.gz",
"platform": null,
"description": "# ipSAE: for binders screening\n\n\n\n## Installation\n\n```bash\npip install ipsae\n```\n\n## Usage\n\nRun `ipSAE` tool from the command line terminal in Linux. It takes the Alphafold2, Alphold3 and Boltz2 multimers PAE file in .json and .pdb or .cif file format as input, and distance cutoff values.\n\n### Command-line Help\n\n```\n$ ipsae --help\n```\n```\nipSAE\nScoring function for interprotein interactions\n-------------------------------------------------\nVersion: 1.0\nAuthor: Samee Ullah\nEmail: sameeullah@bs.qau.edu.pk\nLinkedIn: https://www.linkedin.com/in/ullah-samee/\n-------------------------------------------------\nBased on the original work of Roland Dunbrack.\n\nusage: ipsae [-h] pae_file structure_file [cutoffs ...]\n\nCalculate ipSAE scores for protein-protein interactions\n\npositional arguments:\n pae_file PAE file (JSON or NPZ)\n structure_file Structure file (PDB or CIF)\n cutoffs Optional: PAE and distance cutoff values. Defaults are 15\n for AF2 and 10 for AF3/Boltz1.\n\noptions:\n -h, --help show this help message and exit\n\nExamples:\nFor AlphaFold2:\n ipsae alphafold2_multimer.json alphafold2_model.pdb 15 15\n\nFor AlphaFold3:\n ipsae full_data_0.json model_0.cif 10 10\n\nFor Boltz:\n ipsae pae_model_0.npz Boltz_model.cif 10 10\n```\n\n### Examples\n\n#### AlphaFold2\n\n```bash\nipsae scores.json model.pdb 15 15\n```\ndefault distance cutoffs of 15.\n\n#### AlphaFold3\n\n```bash\nipsae full_data_0.json model_0.cif 10 10\n```\ndefault distance cutoffs of 10.\n\n#### Boltz1\n\n```bash\nipsae pae_model_0.npz model_0.cif 10 10\n```\ndefault distance cutoffs of 10.\n\n## Output Files\n\nThe tool generates three output files:\n\n1. **`<name>_<pae>_<dist>.txt`**: The main output file with chain-chain scores.\n2. **`<name>_<pae>_<dist>_byres.txt`**: By-residue scores.\n3. **`<name>_<pae>_<dist>.pml`**: A PyMOL script for visualizing the ipSAE scores.\n\n### Main Output File Format\n\nThe main output file contains a table with the following columns:\n\n| Chn1 | Chn2 | PAE | Dist | Type | ipSAE | ipSAE_d0chn | ipSAE_d0dom | ipTM_af | ipTM_d0chn | pDockQ | pDockQ2 | LIS | n0res | n0chn | n0dom | d0res | d0chn | d0dom | nres1 | nres2 | dist1 | dist2 | Model |\n|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n\n## Credits\n\nThis tool is based on the original work of Roland Dunbrack.\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Calculate ipSAE scores for protein-protein interactions in AlphaFold2 and AlphaFold3 models",
"version": "1.0.0",
"project_urls": {
"Homepage": "https://github.com/yourusername/ipsae",
"Issues": "https://github.com/yourusername/ipsae/issues",
"Repository": "https://github.com/yourusername/ipsae.git"
},
"split_keywords": [
"protein",
" alphafold",
" bioinformatics",
" structural-biology"
],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "439922de24d3c7b2287508305c9f929610141b544198082ced0490f103c13b5d",
"md5": "8c1fb73851819e98a5053d7d74225208",
"sha256": "5eebc0a16df7922b9cefb4e32abc4041d27e0e0b045a69cc5d4ada209d2ecb05"
},
"downloads": -1,
"filename": "ipsae-1.0.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "8c1fb73851819e98a5053d7d74225208",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 13251,
"upload_time": "2025-09-15T18:11:51",
"upload_time_iso_8601": "2025-09-15T18:11:51.530744Z",
"url": "https://files.pythonhosted.org/packages/43/99/22de24d3c7b2287508305c9f929610141b544198082ced0490f103c13b5d/ipsae-1.0.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "6043b0061882bfa43fa540050970271be297a27f97eec2e4984f4dfc6c75178b",
"md5": "23979097e59a94dd01ca690df4bea855",
"sha256": "cd7c51ac9fa288467ff62b709f9a4c97b5854feba1ecfcfe6ef2ababe9d1d66a"
},
"downloads": -1,
"filename": "ipsae-1.0.0.tar.gz",
"has_sig": false,
"md5_digest": "23979097e59a94dd01ca690df4bea855",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 14031,
"upload_time": "2025-09-15T18:11:53",
"upload_time_iso_8601": "2025-09-15T18:11:53.428572Z",
"url": "https://files.pythonhosted.org/packages/60/43/b0061882bfa43fa540050970271be297a27f97eec2e4984f4dfc6c75178b/ipsae-1.0.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-09-15 18:11:53",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "yourusername",
"github_project": "ipsae",
"github_not_found": true,
"lcname": "ipsae"
}
