Bioinformatics: Difference between revisions

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(→‎Docking: Hydrophobic patches)
 
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* [[Structure based sequence alignment]]
* [[Structure based sequence alignment]]
* [[structural motifs in the PDB]]


== 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]]
* [[Programs for nucleic acid structure analysis|Programs for nucleic acid structure analysis]]
* [[Programs for nucleic acid structure analysis|Programs for nucleic acid structure analysis]]
* [[Morphing]]
* [[Morphing|Morphing and making movies]]
* [[Programs for representing the surface of a channel inside protein]]
* [[Programs for representing the surface of a channel inside protein]]
* [http://www.ebi.ac.uk/thornton-srv/databases/procognate/ database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam]
* [http://www.ebi.ac.uk/thornton-srv/databases/procognate/ database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam]
* [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]] ===
has its own [[Structural superposition|article]].


=== Domain definition ===
=== Domain definition ===
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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 ==

Latest revision as of 10:18, 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]