![[PukiWiki]](image/picc.png "[PukiWiki]")
本家様 https://github.com/martinpacesa/BindCraft
User friendly and accurate binder design pipeline.
(DeepL様翻訳: ユーザーフレンドリーで正確なバインダー設計パイプライン。)
Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta.
Select your target and let the script do the rest of the work and finish once you have enough designs to order!
(同: AlphaFold2バックプロパゲーション、MPNN、PyRosettaを使ったシンプルなバインダー設計パイプライン。
ターゲットを選択し、残りの作業をスクリプトに任せ、注文するのに十分なデザインができたら終了します！)
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2024.10-1[root@rockylinux8 ~]# cat /etc/redhat-release
Rocky Linux release 8.10 (Green Obsidian)
[root@rockylinux8 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 570.86.16 Fri Jan 24 21:25:51 UTC 2025
GCC version: gcc version 8.5.0 20210514 (Red Hat 8.5.0-22) (GCC)
[root@rockylinux8 ~]# /usr/local/cuda/bin/nvcc --version
-bash: /usr/local/cuda/bin/nvcc: No such file or directory <-- cudaライブラリは入れてないです
[root@rockylinux8 ~]# source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
[root@rockylinux8 ~]# cd /apps/
[root@rockylinux8 apps]#
[root@rockylinux8 apps]# git clone https://github.com/martinpacesa/BindCraft
[root@rockylinux8 apps]# cd BindCraft/
[root@rockylinux8 BindCraft]# bash ./install_bindcraft.sh --cuda '12.4' --pkg_manager 'conda'
:
Successfully finished BindCraft installation!
Activate environment using command: "conda activate BindCraft"
:
[root@rockylinux8 BindCraft]#[root@rockylinux8 ~]# source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
[root@rockylinux8 ~]# conda activate BindCraft
(BindCraft) [root@rockylinux8 ~]# conda list | less
:
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.33.0 pyh907856f_0 conda-forge
:
jupyter 1.1.1 pyhd8ed1ab_1 conda-forge
:
jupyterlab 4.3.5 pyhd8ed1ab_0 conda-forge
:
pyrosetta 2025.06+release.029c6a159b py310_0 https://conda.graylab.jhu.edu
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.10.13 hd12c33a_1_cpython conda-forge
:
(BindCraft) [root@rockylinux8 ~]#Environment-modules
「/apps/modulefiles/BindCraft」
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2024.10-1/envs/BindCraft
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib使い方ですが、下記のように git で取得したディレクトリを持ってきて使った方が簡単かな.
[saber@rockylinux8 ~]$ mkdir test && cd test
[saber@rockylinux8 test]$ module use /apps/modulefiles/
[saber@rockylinux8 test]$ module load BindCraft
[saber@rockylinux8 test]$ cp -r /apps/BindCraft .
[saber@rockylinux8 test]$ cd BindCraft/
[saber@rockylinux8 BindCraft]$
[saber@rockylinux8 BindCraft]$ python ./bindcraft.py -h
Available GPUs:
NVIDIA GeForce GTX 10701: gpu
usage: bindcraft.py [-h] --settings SETTINGS [--filters FILTERS] [--advanced ADVANCED]
Script to run BindCraft binder design.
options:
-h, --help show this help message and exit
--settings SETTINGS, -s SETTINGS
Path to the basic settings.json file. Required.
--filters FILTERS, -f FILTERS
Path to the filters.json file used to filter design. If not provided, default will be used.
--advanced ADVANCED, -a ADVANCED
Path to the advanced.json file with additional design settings. If not provided, default will be used.
[saber@rockylinux8 BindCraft]$そしてURLに書かれているサンプルの実行方法ですが、
(修正する)
[saber@rockylinux8 BindCraft]$ vi settings_target/PDL1.json
{
"design_path": "./PDL1/", <-- ここ
"binder_name": "PDL1",
"starting_pdb": "./example/PDL1.pdb", <-- ここ
"chains": "A",
"target_hotspot_residues": "56",
"lengths": [65, 150],
"number_of_final_designs": 100
}
[saber@rockylinux8 BindCraft]$
[saber@rockylinux8 BindCraft]$ python -u ./bindcraft.py --settings './settings_target/PDL1.json' --filters './settings_filters/default_filters.json' --advanced './settings_advanced/default_4stage_multimer.json
Available GPUs:
NVIDIA GeForce GTX 10701: gpu
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x PyRosetta-4 x
x Created in JHU by Sergey Lyskov and PyRosetta Team x
x (C) Copyright Rosetta Commons Member Institutions x
x x
x NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE x
x See LICENSE.PyRosetta.md or email license@uw.edu for details x
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PyRosetta-4 2025 [Rosetta PyRosetta4.conda.ubuntu.cxx11thread.serialization.Ubuntu.python310.Release 2025.06+release.029c6a159b896477003a14f78f472d4cd2cead46 2025-02-04T15:14:13] retrieved from: http://www.pyrosetta.org
Running binder design for target PDL1
Design settings used: default_4stage_multimer
Filtering designs based on default_filters
Starting trajectory: PDL1_l113_s889444
Stage 1: Test Logits
1 models [3] recycles 1 hard 0 soft 0.02 temp 1 loss 12.46 helix 1.54 pae 0.83 i_pae 0.82 con 4.62 i_con 4.20 plddt 0.29 ptm 0.50 i_ptm 0.09 rg 11.87
2 models [2] recycles 1 hard 0 soft 0.04 temp 1 loss 12.19 helix 1.48 pae 0.82 i_pae 0.81 con 4.90 i_con 3.90 plddt 0.34 ptm 0.48 i_ptm 0.13 rg 11.06
3 models [3] recycles 1 hard 0 soft 0.05 temp 1 loss 14.05 helix 0.88 pae 0.74 i_pae 0.79 con 4.68 i_con 4.18 plddt 0.53 ptm 0.49 i_ptm 0.11 rg 16.61
:
:
[saber@rockylinux8 BindCraft]$と実行されます
