CHOP

CHOP dissects protein sequences from entirely sequenced organisms into domain-like fragments to enable sequence-based domain assignment using homology to Protein Data Bank (PDB) structures, Pfam-A domains, and SWISS-PROT entries.

Key Features:

• Input and Output: CHOP accepts protein sequences and outputs lists of domain-like fragments identified by homology to Protein Data Bank (PDB) structures, Pfam-A domains, and SWISS-PROT entries.
• Cutting criteria: Fragment boundaries are defined using cutting points derived from experimental PDB data, expert Pfam-A annotations, and native protein termini.
• Homology Transfer: CHOP employs homology transfer to cross-reference fragments with known structures and domains to support assignment reliability.
• Precomputed Assignments: Precomputed domain assignments exist for many entirely sequenced proteomes to provide ready fragmentation data without recomputation.

Scientific Applications:

• Structural Biology: Facilitates analysis of protein structural organization by providing domain-like fragmentations aligned to known structures and annotations.
• Proteomics: Supports proteomic studies by identifying domains relevant to protein function and interaction analyses.
• Comparative Genomics: Enables comparative analyses by identifying conserved domains across species through homology-based dissections.

Methodology:

CHOP derives cutting points from experimental Protein Data Bank (PDB) data, incorporates expert Pfam-A annotations, considers native protein termini as cut sites, and applies homology transfer to map fragments to PDB structures, Pfam-A domains, and SWISS-PROT entries.