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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]
=== Hydrophobic patches ===
# https://sbgrid.org/software/titles/quilt
# Swiss PDBViewer, detect hydrophobic patches under Tool Surface
# EBI PISA and look for negative delta G
# look at protein-protein interaction and interface dbases
# 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).
# Aggrescan
# 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.
# PASTA
# with pdb structure you can use the Maestro program (from Schrodinger Inc.)
== Other stuff ==
== Other stuff ==
