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Bioinformatics: Difference between revisions
→Docking: Hydrophobic patches
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== Structure only == | == Structure only == | ||
* [[Ligand display]] | |||
* [[Servers for ligand topologies/parameters]] | * [[Servers for ligand topologies/parameters]] | ||
* [[Servers for structure analysis|Servers and programs for protein structure analysis]] | * [[Servers for structure analysis|Servers and programs for protein structure analysis]] | ||
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* [http://robetta.bakerlab.org/alascansubmit.jsp Rosetta Alanine Scanning] each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated | * [http://robetta.bakerlab.org/alascansubmit.jsp Rosetta Alanine Scanning] each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated | ||
* [[solvent-accessible surface]] | * [[solvent-accessible surface]] | ||
* [[topology plots]] | |||
=== [[Structural superposition]] === | === [[Structural superposition]] === | ||
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* [http://autodock.scripps.edu/ AutoDock] - Wiki at https://www.nbcr.net/pub/wiki/index.php?title=AutoDock | * [http://autodock.scripps.edu/ AutoDock] - Wiki at https://www.nbcr.net/pub/wiki/index.php?title=AutoDock | ||
* [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] | |||
=== 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 == | ||