Bioinformatics

From CCP4 wiki
Jump to: navigation, search

Sequence only[edit]

Sequence to structure[edit]

Structure to Sequence[edit]

Structure only[edit]

Structural superposition[edit]

has its own article.

Domain definition[edit]

Functional annotation[edit]

Docking[edit]

Hydrophobic patches[edit]

  1. https://sbgrid.org/software/titles/quilt
  2. Swiss PDBViewer, detect hydrophobic patches under Tool Surface
  3. EBI PISA and look for negative delta G
  4. look at protein-protein interaction and interface dbases
  5. Waltz is an excellent web-server to give very good results on amyloidogenic regions based on sequence stretches (correlate the regions with hydrophobic patches by hydropathy plot obtained from Expasy-Protscale).
  6. Aggrescan
  7. Aggrescan's 3D counterpart http://biocomp.chem.uw.edu.pl/A3D/ - It even allows you to consider whether structures reached by coarse-grained MD are more aggregation-prone than your starting structure.
  8. PASTA
  9. with pdb structure you can use the Maestro program (from Schrodinger Inc.)

Other stuff[edit]