CCM Demo Package

A Python package for computational biology and drug discovery, providing tools for working with biological sequences, structures, and molecular interactions.

Module Structure

📁 apis/

Gateway to biological databases:

• Unified access to PDB, UniProt, NCBI
• Download structures from PDB/AlphaFold DB
• Query protein/gene information
• Upload/download sequence data

📁 binders/

Molecular binding analysis tools:

• Classes:
  • MoleculeBinder: Small molecule binding analysis
  • PeptideBinder: Early stage peptide binding (experimental)
• Features:
  • Pocket detection using fpocket
  • Molecule generation via Pocket2Mol
  • Chemical similarity search (ECFP4, FCFP4, MACCS fingerprints)
  • Structure coordinate calculations
  • RDKit integration

📁 container_runner/

Container orchestration:

• Unified interface for Singularity/Docker
• Job submission to SLURM clusters
• Mount point and volume management
• Container execution monitoring
• Error handling and logging

📁 genome/

Genomic data management:

• Database creation from sequence files
• Gene/transcript/exon queries
• Sequence extraction tools
• Integration with sequence module

📁 knowledge_base/

Biological data organization:

• Structured storage for biological data
• Data format standardization
• Query interfaces and caching
• Version tracking

📁 literature/

Research paper processing:

• Publication searches (PubMed/arXiv)
• Text and metadata extraction
• Reference management
• Content parsing

📁 ranges/

Genomic interval tools:

• Range operations and arithmetic
• Overlap detection
• Coordinate system handling
• BED file processing

📁 sequence/

Biological sequence handlers:

• Sequence data structures
• Multiple sequence alignment
• BLAST integration
• FASTA file operations

📁 structure/

Protein structure tools:

• PDB file operations
• Structure property calculations
• Structure alignment
• Format conversions

Requirements

Dependencies

• Python 3.8+
• BioPython
• RDKit
• PyTorch
• Pandas/NumPy

External Tools

• Singularity/Docker
• MMseqs2
• fpocket
• SLURM (optional)

Development Status

• Container management, sequence, and structure modules are stable
• Binders module is partially implemented
• Other modules under active development

License

[License details pending]

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Developed by the Centre for Computational Medicine