Gough et al. 2001

• "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure"

Concepts

• Homology
• Bayesian Networks
• Markov Models

SCOP database

• Structural Classification of Proteins
• unit of classification is the protein domain
• shape of domain is called the fold
• the fold to which a domain belongs is determined by inspection rather than by software
• Largely manual classification of protein structural domains BASED ON SIMILARITIES OF THEIR STRUCTURE AND AMINO ACID SEQUENCES
• proteins with same shapes but having little sequence or functional similarity are placed in different "superfamilies"
  • superfamilies imply very distant common ancestor
• within super families are just regular families with protein groupings that are more closely related
  • same shape
  • some similarity of sequence and/or function
  • assumed to have a closer common ancestor
• data comes from Protein Data Bank - repository of 3D structural data of large biological molecules, shapes determined by x-ray crystallography or Nuclear Magnetic Resonance Spectroscopy (NMR spectroscopy) of proteins

Vocab

• structural domain - part of a protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded
  • the building blocks of more complex proteins