Bioinformatics

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

DockingEdit

Hydrophobic patchesEdit

  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 stuffEdit