Interface analysis servers - Revision history

Eric Martz: /* LPC/CSU */

2015-09-22T22:58:30Z

LPC/CSU

← Older revision		Revision as of 22:58, 22 September 2015
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	[http://curie.utmb.edu/prosurf.html InterProSurf] operates on entries in the [[PDB]], or uploaded [[atomic coordinate file]]s. Reports numbers of surface and buried atoms for each chain, and areas for each residue deemed to be in the interface. Terms are not defined or explained.		[http://curie.utmb.edu/prosurf.html InterProSurf] operates on entries in the [[PDB]], or uploaded [[atomic coordinate file]]s. Reports numbers of surface and buried atoms for each chain, and areas for each residue deemed to be in the interface. Terms are not defined or explained.

			==PDBparam==

			[http://www.iitm.ac.in/bioinfo/pdbparam/index.html PDBparam] calculates and lists (as text):
			#Identifcation of binding sites
			#Inter-residue interactions
			#Secondary structure propensities
			#Physicochemical properties

	==LPC/CSU==		==LPC/CSU==

Eric Martz at 00:08, 27 January 2015

2015-01-27T00:08:59Z

← Older revision		Revision as of 00:08, 27 January 2015
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	The purpose of this article is to list and evaluate servers that analyze interfaces within molecular models, such as protein-protein, DNA-protein, RNA-protein, and ligand-protein interfaces.		The purpose of this article is to list and evaluate servers that analyze interfaces within molecular models, such as protein-protein, DNA-protein, RNA-protein, and ligand-protein interfaces. This page does not list ''prediction'' servers.

	==COCOMAPS==		==COCOMAPS==

Eric Martz: /* InterProSurf */

2015-01-26T23:50:24Z

InterProSurf

← Older revision		Revision as of 23:50, 26 January 2015
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	==InterProSurf==		==InterProSurf==

	[http://curie.utmb.edu/prosurf.html InterProSurf] operates on entries in the [[PDB]], or uploaded [[atomic coordinate file]]s.		[http://curie.utmb.edu/prosurf.html InterProSurf] operates on entries in the [[PDB]], or uploaded [[atomic coordinate file]]s. Reports numbers of surface and buried atoms for each chain, and areas for each residue deemed to be in the interface. Terms are not defined or explained.

	==LPC/CSU==		==LPC/CSU==

Eric Martz: /* LPC/CSU */

2015-01-26T23:46:40Z

LPC/CSU

← Older revision		Revision as of 23:46, 26 January 2015
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	*Residue counts and inter-atomic distances are tabulated, but neither surface nor interfacial atom counts (in contrast to PISA).		*Residue counts and inter-atomic distances are tabulated, but neither surface nor interfacial atom counts (in contrast to PISA).

			==InterProSurf==

			[http://curie.utmb.edu/prosurf.html InterProSurf] operates on entries in the [[PDB]], or uploaded [[atomic coordinate file]]s.

	==LPC/CSU==		==LPC/CSU==

Eric Martz: /* Comments */

2015-01-26T23:40:36Z

Comments

← Older revision		Revision as of 23:40, 26 January 2015
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	*Note that the ''Table of minimum distances'' lists only the minimum interatomic distance for each pair of residues, not all interatomic distances. The list of ''all'' can be obtained by clicking ''Open table'' under ''Distance table''. However it is not filterable or sortable at the time of this writing (March, 2012).		*Note that the ''Table of minimum distances'' lists only the minimum interatomic distance for each pair of residues, not all interatomic distances. The list of ''all'' can be obtained by clicking ''Open table'' under ''Distance table''. However it is not filterable or sortable at the time of this writing (March, 2012).

			*Residue counts and inter-atomic distances are tabulated, but neither surface nor interfacial atom counts (in contrast to PISA).

	==LPC/CSU==		==LPC/CSU==

Eric Martz: /* PISA */

2015-01-26T23:27:29Z

PISA

← Older revision		Revision as of 23:27, 26 January 2015
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	[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable. '''Click on a row number''' to see full details for any interacting pair of entities. For each chain in a pair of contacting chains, or ligand-chain interaction, it reports total surface area, interfacial area, numbers and percentages of atoms and residues on the surface and in the interface, and numbers of disulfide and hydrogen bonds and salt bridges in the interface, and interfacial free energy changes. There is also an annotated list of all residues in each chain.		[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable. '''Click on a row number''' to see full details for any interacting pair of entities. For each chain in a pair of contacting chains, or ligand-chain interaction, it reports total surface area, interfacial area, numbers and percentages of atoms and residues on the surface and in the interface, and numbers of disulfide and hydrogen bonds and salt bridges in the interface, and interfacial free energy changes. There is also an annotated list of all residues in each chain.

			Most terms are defined with pop-up boxes, but methods are not described on the website.

	Details are reported only for pairs of entities. If one wanted to know the total number of contacting atoms on one chain that is contacting multiple other chains, one would have to add them up manually.		Details are reported only for pairs of entities. If one wanted to know the total number of contacting atoms on one chain that is contacting multiple other chains, one would have to add them up manually.

Eric Martz: /* PISA */

2015-01-26T23:15:52Z

PISA

← Older revision		Revision as of 23:15, 26 January 2015
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	==PISA==		==PISA==

	[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable. '''Click on a row number''' to see full details for any interacting pair of entities. For each chain in a pair of contacting chains, or ligand-chain interaction, it reports total surface area, interfacial area, numbers and percentages of atoms and residues on the surface and in the interface, and numbers of disulfide and hydrogen bonds and salt bridges in the interface, and interfacial free energy changes.		[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable. '''Click on a row number''' to see full details for any interacting pair of entities. For each chain in a pair of contacting chains, or ligand-chain interaction, it reports total surface area, interfacial area, numbers and percentages of atoms and residues on the surface and in the interface, and numbers of disulfide and hydrogen bonds and salt bridges in the interface, and interfacial free energy changes. There is also an annotated list of all residues in each chain.

	Details are reported only for pairs of entities. If one wanted to know the total number of contacting atoms on one chain that is contacting multiple other chains, one would have to add them up manually.		Details are reported only for pairs of entities. If one wanted to know the total number of contacting atoms on one chain that is contacting multiple other chains, one would have to add them up manually.

Eric Martz: /* PISA */

2015-01-26T23:14:39Z

PISA

← Older revision		Revision as of 23:14, 26 January 2015
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	==PISA==		==PISA==

	[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable.		[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable. '''Click on a row number''' to see full details for any interacting pair of entities. For each chain in a pair of contacting chains, or ligand-chain interaction, it reports total surface area, interfacial area, numbers and percentages of atoms and residues on the surface and in the interface, and numbers of disulfide and hydrogen bonds and salt bridges in the interface, and interfacial free energy changes.

			Details are reported only for pairs of entities. If one wanted to know the total number of contacting atoms on one chain that is contacting multiple other chains, one would have to add them up manually.

	==See Also==		==See Also==

Eric Martz: /* PISA */

2015-01-26T23:00:04Z

PISA

← Older revision		Revision as of 23:00, 26 January 2015
Line 20:		Line 20:
	==PISA==		==PISA==

	[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric ~~units~~]] and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable.		[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric unit]]s and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable.

	==See Also==		==See Also==

Eric Martz: /* PISA */

2015-01-26T22:59:48Z

PISA

← Older revision		Revision as of 22:59, 26 January 2015
Line 20:		Line 20:
	==PISA==		==PISA==

	[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]].		[http://www.ebi.ac.uk/pdbe/pisa/ The PISA server] (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own [[atomic coordinate file]]. PISA analyses interfaces occurring in [[asymmetric units]] and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable.

	==See Also==		==See Also==