Difference between revisions of "Bioinformatics"

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(→‎Structure only: topology plots)
(→‎Docking: Hydrophobic patches)
 
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* [http://blaster.docking.org/start.shtml DockBlaster] - runs DOCK 3.5.54; there's a [http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_Blaster:FAQ wiki]
 
* [http://blaster.docking.org/start.shtml DockBlaster] - runs DOCK 3.5.54; there's a [http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_Blaster:FAQ wiki]
 
* [http://bioinfo3d.cs.tau.ac.il/SymmDock/ SymmDock]
 
* [http://bioinfo3d.cs.tau.ac.il/SymmDock/ SymmDock]
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 +
=== Hydrophobic patches ===
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# https://sbgrid.org/software/titles/quilt
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# Swiss PDBViewer, detect hydrophobic patches under Tool Surface
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# EBI PISA and look for negative delta G
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# look at protein-protein interaction and interface dbases
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# 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).
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# Aggrescan
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# 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.
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# PASTA
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# with pdb structure you can use the Maestro program (from Schrodinger Inc.)
  
 
== Other stuff ==
 
== Other stuff ==

Latest revision as of 09:18, 27 July 2017

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]

  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 | edit source]