Bioinformatics - Revision history

Kay: /* Docking */ Hydrophobic patches

2017-07-27T09:18:41Z

Docking: Hydrophobic patches

@@ Line 53: / Line 53: @@
 * [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]
 == Other stuff ==

Kay: /* Structure only */ topology plots

2013-03-12T21:14:23Z

Structure only: topology plots

← Older revision		Revision as of 23:14, 12 March 2013
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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]] ===

Kay: /* Structure only */

2012-01-21T12:14:37Z

Structure only

← Older revision		Revision as of 14:14, 21 January 2012
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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]]

Kay: /* Docking */

2011-06-10T17:24:33Z

Docking

← Older revision		Revision as of 19:24, 10 June 2011
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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]

	== Other stuff ==		== Other stuff ==

Kay: /* Structure only */

2011-04-15T06:50:15Z

Structure only

← Older revision		Revision as of 08:50, 15 April 2011
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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]]

			=== [[Structural superposition]] ===
			has its own [[Structural superposition\|article]].

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

Kay: /* Structure to Sequence */

2011-04-06T19:54:51Z

Structure to Sequence

← Older revision		Revision as of 21:54, 6 April 2011
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	* [[Structure based sequence alignment]]		* [[Structure based sequence alignment]]
			* [[structural motifs in the PDB]]

	== Structure only ==		== Structure only ==

Kay: /* Structure only */

2011-03-09T08:51:00Z

Structure only

← Older revision		Revision as of 10:51, 9 March 2011
Line 17:		Line 17:
	* [[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]

Kay: /* Structure only */

2010-11-03T15:04:46Z

Structure only

← Older revision		Revision as of 17:04, 3 November 2010
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	* [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]]

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

Kay: /* Domain definition */

2010-09-04T18:25:31Z

Domain definition

← Older revision		Revision as of 20:25, 4 September 2010
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	* A collection of links to structure-based domain parsers is at http://binf.gmu.edu/ttaylor/homepagelinks.html		* A collection of links to structure-based domain parsers is at http://binf.gmu.edu/ttaylor/homepagelinks.html
	* Domain boundaries are available through RCSB PDB RESTful web services described at: http://www.pdb.org/pdb/software/rest.do. For example, the URL http://www.pdb.org/pdb/rest/das/pdbchainfeatures/features?segment=1AJH.A returns an XML file with SCOP, CATH, DP, PDP, PFAM, InterPro domain boundaries, plus secondary structure information by DSSP, STRIDE, and the structure author.		* Domain boundaries are available through RCSB PDB RESTful web services described at: http://www.pdb.org/pdb/software/rest.do. For example, the URL http://www.pdb.org/pdb/rest/das/pdbchainfeatures/features?segment=1AJH.A returns an XML file with SCOP, CATH, DP, PDP, PFAM, InterPro domain boundaries, plus secondary structure information by DSSP, STRIDE, and the structure author.
			* In the sequence tab for each PDB entry, (for example, http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AJH), the domain assignment from SCOP, DP, CATH etc. are given.

	=== Functional annotation ===		=== Functional annotation ===

Kay: /* Structure only */ domains

2010-09-04T18:24:01Z

Structure only: domains

← Older revision		Revision as of 20:24, 4 September 2010
Line 21:		Line 21:
	* [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
	* [http://pdomains.sdsc.edu] offering an interface for comparing a number of different methods for ''automatic domain definition''
			=== Domain definition ===

			* http://pdomains.sdsc.edu offering an interface for comparing a number of different methods for ''automatic domain definition''. For domain interfaces [http://141.30.193.6/scoppi/ SCOPPI] may be helpful.
			* http://www.ebi.ac.uk/pdbe/docs/sifts/ a list of tab delimited files that contain all the information for each chain in the PDB. The information is also available per residue in XML format that contain additional annotation. These files are updated every week.
			* A collection of links to structure-based domain parsers is at http://binf.gmu.edu/ttaylor/homepagelinks.html
			* Domain boundaries are available through RCSB PDB RESTful web services described at: http://www.pdb.org/pdb/software/rest.do. For example, the URL http://www.pdb.org/pdb/rest/das/pdbchainfeatures/features?segment=1AJH.A returns an XML file with SCOP, CATH, DP, PDP, PFAM, InterPro domain boundaries, plus secondary structure information by DSSP, STRIDE, and the structure author.


	=== Functional annotation ===		=== Functional annotation ===