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https://github.com/PDB-REDO/alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://github.com/PDB-REDO/alphafill

Last synced: about 1 month ago
JSON representation

Host: GitHub
URL: https://github.com/PDB-REDO/alphafill
Owner: PDB-REDO
License: bsd-2-clause
Created: 2021-11-24T10:57:46.000Z (about 3 years ago)
Default Branch: trunk
Last Pushed: 2024-04-24T15:30:53.000Z (8 months ago)
Last Synced: 2024-08-03T14:08:47.358Z (4 months ago)
Language: C++
Homepage: https://alphafill.eu
Size: 2.44 MB
Stars: 89
Watchers: 7
Forks: 17
Open Issues: 0
Metadata Files:
- Readme: README.md
- Changelog: changelog
- License: LICENSE

Awesome Lists containing this project

awesome-protein-design-software - AlphaFill - [web app](https://alphafill.eu/) - [paper](https://www.nature.com/articles/s41592-022-01685-y) (Peptide and ligand binding)

README

[![github CI](https://github.com/pdb-redo/alphafill/actions/workflows/cmake-multi-platform.yml/badge.svg)](https://github.com/pdb-redo/alphafill/actions)
[![GitHub License](https://img.shields.io/github/license/pdb-redo/alphafill)](https://github.com/pdb-redo/alphafill/LICENSE)

# AlphaFill

**AlphaFill** is an algorithm based on sequence and structure similarity that “transplants”
missing compounds to the [AlphaFold models](https://alphafold.ebi.ac.uk/). By adding the molecular context to the protein structures, the
models can be more easily appreciated in terms of function and structure integrity.

## Building

In order to build alphafill, you need to have a modern C++ compiler (c++17), a recent version of [cmake](https://cmake.org/) and the following libraries installed:

- [Libzeep](https://github.com/mhekkel/libzeep) version 6.0.11 or higher
- [libcif++](https://github.com/PDB-REDO/libcifpp) version 6.0.0 or higher
- [libmcfp](https://github.com/mhekkel/libmcfp) version 1.2.4 or higher

The default assumes you only want to process predicted models locally. If you want to build the web application environment you will have to install the following as well:

- libpq, the PostgreSQL library
- [libpqxx](http://www.pqxx.org/) version 7.2 or higher
- [yarn](https://yarnpkg.com/) to package the data for the web interface.
- [mrc](https://github.com/mhekkel/mrc) to package all the runtime data into resources in the final excutable. This is optional and will not work on *macOS*.

Once all the requirements are met, building is as simple as:

```console
git clone https://github.com/PDB-REDO/alphafill
cd alphafill
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build build
ctest --test-dir build
cmake --install build
```

## Configuration

After installing alphafill as described in the previous section, a default configuration file has been written to your */etc* directory. The install command should have told you which file to edit.

In this configuration file you should at least specify the following three paths:

- pdb-dir

This is the directory containing your copy of the entire PDB or PDB-REDO's XXXX_final.cif files.

- pdb-fasta

The path to the file containing the sequences from the PDB files in FastA format. This file is generated by the `alphafill create-index` command.

- ligands

The path to the file containing the ligands that need to be included in processing. A default file is provided.

- db-dir

The directory containing the eventual alphafill files. This directory only needs to be specified if you build a webserver.

### alphafill

Before you can process your models, you will have to build the PDB FastA file using the create-index command:

```console
alphafill create-index
```

Processing a model is then as easy as:

```console
alphafill process /srv/data/afdb/cif/AF-XXX.cif.gz /srv/data/af-filled/AF-XXX.cif.gz
```

Typical running time is less than 2 minutes but varies depending on the number of transplants.

### web interface

To enable the web interface you needed to have the BUILD_WEB_APPLICATION option ON during configuration.

Before running the web application, you need to create a PostgreSQL database. This database will contain the statistics for the processed files in `db-dir`. The connection details for this databank should be recorded in the alphafill.conf file. The database can be filled with the `alphafill rebuild-db` command.

After this setting up, you can start a web server using `alphafill server start`. Use `alphafill server status` to find the status of the server and `alphafill server stop` to stop it again. In this case the alphafill server runs as a daemon and log files will be written to /var/log/alphafill/. You can also start with the extra --no-daemon option and then the server will run in the foreground.