计算生物学环境搭建

Python Setup

Anaconda

1. install conda in Ubuntu/Debian

   # Download latest Anaconda (2024.02-1)
   wget https://repo.anaconda.com/archive/Anaconda3-2024.02-1-Linux-x86_64.sh
   bash Anaconda3-2024.02-1-Linux-x86_64.sh

2. install conda in Fedora/RHEL/CentOS

   # Method 1: Direct download and install
   wget https://repo.anaconda.com/archive/Anaconda3-2024.02-1-Linux-x86_64.sh
   bash Anaconda3-2024.02-1-Linux-x86_64.sh
   
   # Method 2: Using dnf package manager (recommended for Fedora)
   sudo dnf install conda
   # or install Anaconda Navigator
   sudo dnf install anaconda-navigator
   
   # Method 3: Using Mambaforge (lightweight alternative)
   curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
   bash Mambaforge-Linux-x86_64.sh

Python environment

1. create a new environment with specific Python version

   conda create -n myenv python=3.12

2. create a new environment with specific Python version and packages

   conda create -n myenv python=3.12 numpy pandas matplotlib

3. create a new environment with specific Python version and packages from a YAML file

   conda env create -f environment.yml

4. remove an environment

   conda env remove -n myenv

5. copy an environment

   conda create -n newenv --clone myenv

6. export an environment to a YAML file

   conda env export -n myenv > environment.yml

Docking Setup

AutoDock Vina

vina available at https://github.com/ccsb-scripps/AutoDock-Vina

• different versions will have different arguments and scoring value!

AutoDock-GPU

AutoDock available at https://github.com/ccsb-scripps/AutoDock-GPU

• For larger ligands, increase MAX_NUM_OF_ROTBONDS in common/defines.h and recompile. See https://github.com/ccsb-scripps/AutoDock-GPU/issues/205.

ADFRSuite

ADFRSuite available at https://ccsb.scripps.edu/adfr/downloads/

• external scripts available at https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/autodock_scripts
• or use meeko: pip install -U numpy scipy rdkit vina meeko gemmi prody, see https://autodock-vina.readthedocs.io/en/latest/docking_requirements.html.

AutoDock Tools

AutoDock Tools available at https://autodocksuite.scripps.edu/adt/

GROMACS Setup

Install

• download: https://manual.gromacs.org
• Installation guide: https://manual.gromacs.org/documentation/current/install-guide/index.html