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Sequence only[edit | edit source]

Sequence to structure[edit | edit source]

Structure to Sequence[edit | edit source]

Structure only[edit | edit source]

Structural superposition[edit | edit source]

has its own article.

Domain definition[edit | edit source]

Functional annotation[edit | edit source]

Docking[edit | edit source]

Hydrophobic patches[edit | edit source]

  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 stuff[edit | edit source]