A Bioinformatics how to...
use publicly available free tools to predict protein structure using comparative modeling

As mentioned in your lecture notes,

The Steps in Comparative (Homology) Modeling

Recognition

• Are there any well characterized proteins similar to my protein?
• Useful tools:
  • BLAST (http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi)
  • PSI-BLAST (from protein blast, in the "Algorithm" section, select PSI-BLAST)
  • PFAM (http://www.sanger.ac.uk/Software/Pfam/search.shtml)
  • FFAS (http://ffas.ljcrf.edu/)

Alignment

• What is the position-by-position target/template equivalence?
• Useful tools:
• The same tools as used in the recognition step. However, different parameters may be used.

Modeling

• What is the detailed 3D structure of my protein?
• Useful tools:
• Freeware/shareware/servers:
  • SwissModel- webserver
  • Modeller (Andrej Sali)- download software
  • Jackal (Barry Honig)- download software
  • SCWRL (Roland Dunbrack)- webserver, download software
• Commericial programs:
  • Accelrys (Insight)
  • Tripos (Sybyl)

Model Analysis

• Is my model any good?
  • Tools to measure model quality
    • Empirical energy based
      • PSQS
      • SwissPDB viewer
    • Geometric quality
      • Procheck, SFCHECK, etc.
  • Other things to consider
    • What is the function (activity, process) of my protein?
    • Does the template have the same or a similar function?
    • If so, how good is the alignment of the active site or residues involved in this function? Are these residues conserved?