Questions to ask about all new structures.

Below is a list of default questions that one might ask about any new protein structure along with the applications we have in the CSB to answer them. Some of these questions may be made irrelevant by specific a priori knowledge you have on your protein but this is a default list.

Click on the APPLICATION for a more detailed discussion of each using the pyrococcus woesei TATA-binding protein solved by Brian Dedecker and Paul Sigler (1PCZ) as an example protein. In most cases below only the A chain from the PDB file was used.

• Is the geometry correct?
  PROCHECK - PostScript Plots and ASCII output
  WHATIF - ASCII output
  
  
• Is the structure similar to something else?
  DALI - Web server returns ASCII list
  CATH - Web server returns HTML list with links
  CE - Combinatorial Extension Finds 3D Similarities
  DEJAVU - Gerard Kleywegt's database search
  VAST - NCBI's structure-structure similarity search service
  
  
• If so, which regions are similar?
  DDMP - Compare CA distance matrices
  
  
• What is the secondary structure?
  RIBBONS - Display
  DEFINE_S - Display and List
  DSSP - List
  
  
• If this is a mutant or different space group or in complex, which residues have changed conformation?
  DDMP - Compare CA Atoms
  COORDCOMP - Compare Side Chain and CA Atoms
  
  
• Does it have unusual electrostatics?
  GRASP - Calculate and display electrostatic potential
  
  
• Is the packing normal?
  OS - Calculate residue packing
  MSP - Calculate cavities
  
  
• What are the possible binding sites?
  APROPOS - Deviations from a convex hull
  SURFNET - Clefts found with spherical probes
  
  
• If an oligomer, what is the buried surface area?
  MSP - Calculate total buried surface area analytically
  GRASP - Display total buried surface area
  INTCHOS - List Occluded Residues in interface