معرفی شرکت ها
appraise-1.2.4
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Scripts and functions needed for for APPARISE.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | appraise-1.2.4 |
| نام | appraise |
| نسخه کتابخانه | 1.2.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Xiaozhe Ding |
| ایمیل نویسنده | xding@caltech.edu |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/appraise/ |
| مجوز | - |
# APPRAISE: Rank binders by structure modeling
***A***utomated ***P***air-wise ***P***eptide-***R***eceptor binding model ***A***nalys***I***s for ***S***creening ***E***ngineered proteins (***APPRAISE***) is a method that predicts the receptor binding propensity of engineered proteins based on high-precision protein structure prediction tools, such as AlphaFold2-multimer. The APPRAISE Python package includes tools for preparing input files and analyzing the modeled structures.
Author: Xiaozhe Ding (Email: dingxiaozhe@gmail.com, xding@caltech.edu; Twitter: [@DingXiaozhe](https://twitter.com/dingxiaozhe?lang=en))
## Getting started without installation
We recommend using APPRAISE remotely by running Colab-APPRAISE notebook on Google Colaboratory, which allows you to access APPRAISE with a **web-based interface**. This notebook guides users through the APPRAISE process step-by-step, with results stored on Google Drive. No need for a local installation when using this notebook.
The basic service of Google Colaboratory is free, although you can choose paid plans to get more stable access to better hardwares.
**How to run Colab-APPRAISE**
1. [Open Colab-APPRAISE notebook in Google Colaboratory](https://colab.research.google.com/github/xz-ding/APPRAISE/blob/main/Colab_APPRAISE.ipynb);
2. Go to "File --> save a copy in Drive" to save a copy of your own;
3. Follow the Quick guide on the top of the notebook, and you can start APPRAISing!
## Local installation
### Environment
Local APPRAISE 1.2 was tested with the following environment:
- MacOS 10.14.6
- Python 3.6.10
- Alphafold-colabfold 2.1.14 (Available [here](https://github.com/sokrypton/ColabFold))
- PyMOL 2.3.3 (Schrodinger LLC.)
- Python packages (will be automatically handled by pip):
- scipy 1.4.1
- numpy 1.18.2
- pandas 1.1.5
- matplotlib 3.2.1
- seaborn 0.11.2
### Installation options
Installation of APPRAISE locally requires pip. In most cases, pip comes with your Python environment. If not, you can [follow the instructions here to install pip](https://pip.pypa.io/en/stable/installation/).
#### Option 1 (recommended)
Install the distribution from PyPI. In the terminal, run:
```
pip install appraise
```
#### Option 2 (back-up)
Download the repository to your local computer and unzip. In the terminal, [change the working folder](https://ss64.com/osx/cd.html) to the directory containing the appraise package folder and setup.py, and run the following line:
```
pip install -e .
```
### Demo
You can find a few demo notebooks that work **locally** in the [demo folder on GitHub](https://github.com/GradinaruLab/APPRAISE/tree/main/demo).
## References
[Manuscript](http://biorxiv.org/content/10.1101/2023.01.11.523680v1)
Xiaozhe Ding\*, Xinhong Chen, Erin E. Sullivan, Timothy F Shay, Viviana Gradinaru\*. APPRAISE: Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling. BioRxiv (2023). \* Corresponding authors.
[Github repository](https://github.com/xz-ding/APPRAISE)
The repository contains the latest version of APPRAISE package, Colab-APPRAISE notebook, and demo notebooks.
## Related resources
[ColabFold](https://github.com/sokrypton/ColabFold)
ColabFold provides a panel of user-friendly tools for structure modeling that are used by APPRAISE.
نیازمندی
| مقدار | نام |
|---|---|
| >=1.4.1 | scipy |
| >=1.18.2 | numpy |
| >=1.1.5 | pandas |
| >=3.2.1 | matplotlib |
| >=0.11.2 | seaborn |
نحوه نصب
نصب پکیج whl appraise-1.2.4:
pip install appraise-1.2.4.whl
نصب پکیج tar.gz appraise-1.2.4:
pip install appraise-1.2.4.tar.gz