Epitopes - Revision history

Wayne Decatur at 00:26, 3 January 2011

2011-01-03T00:26:55Z

← Older revision		Revision as of 00:26, 3 January 2011
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	===ElliPro===		===ElliPro===
	[http://tools.immuneepitope.org/tools/ElliPro/iedb_input ElliPro] is a web-tool that implements ~~Thornton~~'s ~~method~~ and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. The methods are published<ref>PMID:19055730</ref>.		[http://tools.immuneepitope.org/tools/ElliPro/iedb_input ElliPro] is a web-tool that implements a method for identifying continuous epitopes in the protein regions protruding from the protein's globular surface and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. The methods are published<ref>PMID:19055730</ref>.

	===EpiSearch===		===EpiSearch===

Wayne Decatur: added ElliPro

2011-01-02T22:36:25Z

added ElliPro

← Older revision		Revision as of 22:36, 2 January 2011
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	'''In alphabetical order:'''		'''In alphabetical order:'''

			===ElliPro===
			[http://tools.immuneepitope.org/tools/ElliPro/iedb_input ElliPro] is a web-tool that implements Thornton's method and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. The methods are published<ref>PMID:19055730</ref>.

	===EpiSearch===		===EpiSearch===

Eric Martz: /* Epitope Prediction Servers */ polishing

2009-05-30T05:23:10Z

Epitope Prediction Servers: polishing

← Older revision		Revision as of 05:23, 30 May 2009
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	In the absence of the crystal structure of an antibody:antigen complex, a common way to identify the epitope recognized by a particular antibody is to display random peptides (for example, using [http://en.wikipedia.org/wiki/Phage_display phage display libraries]), and then to identify the sequences of the peptides with the highest affinity for the antibody. These sequences can then be used to predict where the epitope lies on the native protein, taking into account that the epitope on the native protein may be discontinuous. In order to use this strategy, the 3D structure of the protein antigen must be known.		In the absence of the crystal structure of an antibody:antigen complex, a common way to identify the epitope recognized by a particular antibody is to display random peptides (for example, using [http://en.wikipedia.org/wiki/Phage_display phage display libraries]), and then to identify the sequences of the peptides with the highest affinity for the antibody. These sequences can then be used to predict where the epitope lies on the native protein, taking into account that the epitope on the native protein may be discontinuous. In order to use this strategy, the 3D structure of the protein antigen must be known.

			'''In alphabetical order:'''

	===EpiSearch===		===EpiSearch===

Eric Martz: /* Epitope Prediction Servers */ adding content

2009-05-30T05:21:31Z

Epitope Prediction Servers: adding content

← Older revision		Revision as of 05:21, 30 May 2009
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	==Epitope Prediction Servers==		==Epitope Prediction Servers==

			Over a dozen servers that predict epitopes are available ([http://www.google.com/#hl=en&q=epitope+prediction+server Google Search for "epitope prediction server"]). Only a few of these are listed below. Please help by adding more, with descriptions. It would also be very useful to have performance comparisons.

	In the absence of the crystal structure of an antibody:antigen complex, a common way to identify the epitope recognized by a particular antibody is to display random peptides (for example, using [http://en.wikipedia.org/wiki/Phage_display phage display libraries]), and then to identify the sequences of the peptides with the highest affinity for the antibody. These sequences can then be used to predict where the epitope lies on the native protein, taking into account that the epitope on the native protein may be discontinuous. In order to use this strategy, the 3D structure of the protein antigen must be known.		In the absence of the crystal structure of an antibody:antigen complex, a common way to identify the epitope recognized by a particular antibody is to display random peptides (for example, using [http://en.wikipedia.org/wiki/Phage_display phage display libraries]), and then to identify the sequences of the peptides with the highest affinity for the antibody. These sequences can then be used to predict where the epitope lies on the native protein, taking into account that the epitope on the native protein may be discontinuous. In order to use this strategy, the 3D structure of the protein antigen must be known.

Eric Martz: /* Epitope Prediction Servers */ adding content

2009-05-30T05:13:32Z

Epitope Prediction Servers: adding content

← Older revision		Revision as of 05:13, 30 May 2009
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	==Epitope Prediction Servers==		==Epitope Prediction Servers==

	In the absence of the crystal structure of an antibody:antigen complex, a common way to identify the epitope recognized by a particular antibody is to display random peptides (for example, using [http://en.wikipedia.org/wiki/Phage_display phage display libraries]), and then to identify the sequences of the peptides with the highest affinity for the antibody. These sequences can then be used to predict where the epitope lies on the native protein, taking into account that the epitope on the native protein may be discontinuous. In this strategy, the 3D structure of the protein antigen must be known.		In the absence of the crystal structure of an antibody:antigen complex, a common way to identify the epitope recognized by a particular antibody is to display random peptides (for example, using [http://en.wikipedia.org/wiki/Phage_display phage display libraries]), and then to identify the sequences of the peptides with the highest affinity for the antibody. These sequences can then be used to predict where the epitope lies on the native protein, taking into account that the epitope on the native protein may be discontinuous. In order to use this strategy, the 3D structure of the protein antigen must be known.

	===EpiSearch===		===EpiSearch===
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	===Epitopia Server===		===Epitopia Server===
	The [http://epitopia.tau.ac.il/ Epitopia Server] predicts immunogenic regions in general. It will accept either a protein sequence, or a 3D protein structure. It "implements a machine learning scheme to rank individual amino acids in the protein, according to their potential of eliciting a humoral immune response". (Thus, it does not require a list of peptides that bind to an antibody of interest.) When a 3D model is submitted, it can be visualized in Jmol colored by predicted immunogenicity. The methods are published<ref>PMID:18947876</ref>.		The [http://epitopia.tau.ac.il/ Epitopia Server] predicts immunogenic regions in general. It will accept either a protein sequence, or a 3D protein structure. It "implements a machine learning scheme to rank individual amino acids in the protein, according to their potential of eliciting a humoral immune response". (Thus, it does not require a list of peptides that bind to an antibody of interest.) When a 3D model is submitted, it can be visualized in [[FirstGlance in Jmol]] colored by predicted immunogenicity. The methods are published<ref>PMID:18947876</ref>.

			===Pepitope Server===
			The [http://pepitope.tau.ac.il/ Pepitope Server] predicts epitopes on the surface of a 3D protein antigen model, based on a list of peptides that bind to the antibody. The 3D model can be a [[PDB code]] or uploaded. Results can be visualized interactively in [[FirstGlance in Jmol]]. The algorithm is also available as a stand-alone program called ''PepSurf'' (with C++ source), licensed for non-commercial use by Tel-Aviv University. The methods are published<ref>PMID: 17977889</ref>.

	==References and Notes==		==References and Notes==

	<references />		<references />

Eric Martz: /* Epitopia Server */ adding content

2009-05-30T05:01:46Z

Epitopia Server: adding content

← Older revision		Revision as of 05:01, 30 May 2009
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	===Epitopia Server===		===Epitopia Server===
	The [http://epitopia.tau.ac.il/ Epitopia Server] predicts immunogenic regions in general. It will accept either a protein sequence, or a 3D protein structure. It "implements a machine learning scheme to rank individual amino acids in the protein, according to their potential of eliciting a humoral immune response". (Thus, it does not require a list of peptides that bind to an antibody of interest.) When a 3D model is submitted, it can be visualized in Jmol colored by predicted immunogenicity.		The [http://epitopia.tau.ac.il/ Epitopia Server] predicts immunogenic regions in general. It will accept either a protein sequence, or a 3D protein structure. It "implements a machine learning scheme to rank individual amino acids in the protein, according to their potential of eliciting a humoral immune response". (Thus, it does not require a list of peptides that bind to an antibody of interest.) When a 3D model is submitted, it can be visualized in Jmol colored by predicted immunogenicity. The methods are published<ref>PMID:18947876</ref>.

	==References and Notes==		==References and Notes==

	<references />		<references />

Eric Martz: /* Epitope Prediction Servers */ adding content

2009-05-30T04:57:16Z

Epitope Prediction Servers: adding content

← Older revision		Revision as of 04:57, 30 May 2009
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	===Epitopia Server===		===Epitopia Server===
	The [http://epitopia.tau.ac.il/ Epitopia Server]		The [http://epitopia.tau.ac.il/ Epitopia Server] predicts immunogenic regions in general. It will accept either a protein sequence, or a 3D protein structure. It "implements a machine learning scheme to rank individual amino acids in the protein, according to their potential of eliciting a humoral immune response". (Thus, it does not require a list of peptides that bind to an antibody of interest.) When a 3D model is submitted, it can be visualized in Jmol colored by predicted immunogenicity.

	==References and Notes==		==References and Notes==

	<references />		<references />

Eric Martz: polishing

2009-05-30T04:49:43Z

polishing

← Older revision		Revision as of 04:49, 30 May 2009
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	An epitope is the portion of the surface of an antigen that binds to an [[Antibody\|antibody]], or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a [[X-~~Ray Crystallography~~\|crystal structure]] of the antibody:antigen complex, where the contacts are evident. There are several [[#Epitope Prediction Servers\|servers that attempt to predict epitopes]].		An epitope is the portion of the surface of an antigen that binds to an [[Antibody\|antibody]], or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a [[X-ray crystallography\|crystal structure]] of the antibody:antigen complex, where the contacts are evident. There are several [[#Epitope Prediction Servers\|servers that attempt to predict epitopes]].

	==Terminology==		==Terminology==

Eric Martz: polishing

2009-05-30T04:49:19Z

polishing

← Older revision		Revision as of 04:49, 30 May 2009
Line 1:		Line 1:
	An epitope is the portion of the surface of an antigen that binds to an [[Antibody\|antibody]], or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a [[X-Ray Crystallography\|crystal structure] of the antibody:antigen complex, where the contacts are evident. There are several [[#Epitope Prediction Servers\|servers that attempt to predict epitopes]].		An epitope is the portion of the surface of an antigen that binds to an [[Antibody\|antibody]], or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a [[X-Ray Crystallography\|crystal structure]] of the antibody:antigen complex, where the contacts are evident. There are several [[#Epitope Prediction Servers\|servers that attempt to predict epitopes]].

	==Terminology==		==Terminology==

Eric Martz: polishing

2009-05-30T04:48:53Z

polishing

← Older revision		Revision as of 04:48, 30 May 2009
Line 1:		Line 1:
	An epitope is the portion of the surface of an antigen that binds to an [[Antibody\|antibody]], or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a crystal structure of the antibody:antigen complex, where the contacts are evident. There are several [[#Epitope Prediction Servers\|servers that attempt to predict epitopes]].		An epitope is the portion of the surface of an antigen that binds to an [[Antibody\|antibody]], or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a [[X-Ray Crystallography\|crystal structure] of the antibody:antigen complex, where the contacts are evident. There are several [[#Epitope Prediction Servers\|servers that attempt to predict epitopes]].

	==Terminology==		==Terminology==