Revision as of 09:18, 27 July 2017 by Kay (talk | contribs) (→‎Docking: Hydrophobic patches)
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Sequence onlyEdit

Sequence to structureEdit

Structure to SequenceEdit

Structure onlyEdit

Structural superpositionEdit

has its own article.

Domain definitionEdit

Functional annotationEdit


Hydrophobic patchesEdit

  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 - 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 stuffEdit