Complete installation guide for all software and tools needed for the protein design course
Package and environment management for scientific computing
Check installation:
conda --versionSet up isolated environment for protein design work
conda create -n protein-design python=3.9conda activate protein-designInstall essential Python packages for biological computing
pip install biopython numpy pandas matplotlib scipypip install jupyter notebook ipykernelAdd molecular dynamics and visualization packages
conda install -c conda-forge mdanalysisconda install -c conda-forge pymol-open-sourceTest that all packages are working correctly
python -c "import Bio; print('BioPython:', Bio.__version__)"python -c "import MDAnalysis; print('MDAnalysis:', MDAnalysis.__version__)"Biological computation library for sequence analysis
Numerical computing with multi-dimensional arrays
Data manipulation and analysis library
2D plotting library for creating visualizations
Installation:
pip install matplotlibTest import:
import matplotlib; print(matplotlib.__version__)Analysis of molecular dynamics trajectories
Installation:
pip install MDAnalysisTest import:
import MDAnalysis; print(MDAnalysis.__version__)Molecular visualization system for 3D structure analysis
Installation:
Academic license available, open-source version via conda
conda install -c conda-forge pymol-open-sourceNote: Academic users can get free educational license
Next-generation molecular visualization program
Installation:
Free download for academic use
Download from UCSF websiteNote: Excellent for cryo-EM and large structure visualization
Molecular dynamics simulation package
Installation:
Compile from source or use package manager
conda install -c conda-forge gromacsNote: GPU acceleration available for faster simulations
Visual Molecular Dynamics for trajectory analysis
Installation:
Free registration required for download
Download from UIUC websiteNote: Excellent for MD trajectory visualization and analysis