Practical Guide to Homology Modeling - Revision history

Eric Martz at 20:37, 20 October 2024

2024-10-20T20:37:25Z

← Older revision		Revision as of 20:37, 20 October 2024
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	<table style="background:#ffff80;"><tr><td>		<table style="background:#ffff80;"><tr><td>
	<big>Homology modeling has become largely obsolete since the success of structure prediction by [[AlphaFold]] and other AI prediction systems. Rather than starting here, we suggest starting at [[How To Find A Structure]].		<big>Homology modeling has become largely obsolete since the 2020 success of structure prediction by [[AlphaFold]] and other AI prediction systems. Rather than starting here, we suggest starting at [[How To Find A Structure]].
	</big>		</big>
	<br><br>		<br><br>

Eric Martz at 20:37, 20 October 2024

2024-10-20T20:37:05Z

← Older revision		Revision as of 20:37, 20 October 2024
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	<table style="background:#ffff80;"><tr><td>		<table style="background:#ffff80;"><tr><td>
	Homology modeling has become largely obsolete since the success of structure prediction by [[AlphaFold]] and other AI prediction systems. Rather than starting here, we suggest starting at [[How To Find A Structure]].		<big>Homology modeling has become largely obsolete since the success of structure prediction by [[AlphaFold]] and other AI prediction systems. Rather than starting here, we suggest starting at [[How To Find A Structure]].
			</big>
	<br><br>		<br><br>
	Many assertions in this article are lacking literature citations. Help improving documentation in this article will be appreciated. Wikipedia's article on [http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] is well documented, although more technical and less of a practical guide than the present article.</td></tr></table>		Many assertions in this article are lacking literature citations. Help improving documentation in this article will be appreciated. Wikipedia's article on [http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] is well documented, although more technical and less of a practical guide than the present article.</td></tr></table>

Eric Martz at 20:35, 20 October 2024

2024-10-20T20:35:23Z

← Older revision		Revision as of 20:35, 20 October 2024
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	<table style="background:#ffff80;"><tr><td>Many assertions in this article are lacking literature citations. Help improving documentation in this article will be appreciated. Wikipedia's article on [http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] is well documented, although more technical and less of a practical guide than the present article.</td></tr></table>		<table style="background:#ffff80;"><tr><td>
			Homology modeling has become largely obsolete since the success of structure prediction by [[AlphaFold]] and other AI prediction systems. Rather than starting here, we suggest starting at [[How To Find A Structure]].
			<br><br>
			Many assertions in this article are lacking literature citations. Help improving documentation in this article will be appreciated. Wikipedia's article on [http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] is well documented, although more technical and less of a practical guide than the present article.</td></tr></table>

	== Terminology ==		== Terminology ==

Jaime Prilusky at 17:54, 13 February 2022

2022-02-13T17:54:39Z

← Older revision		Revision as of 17:54, 13 February 2022
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	==== FoldIndex ====		==== FoldIndex ====

	The [~~http~~://~~bip~~.~~weizmann~~.~~ac.il/fldbin/findex~~ FoldIndex server] is a useful adjunct to the MobiDB report, since it is not included in that report.		The [https://fold.proteopedia.org FoldIndex server] is a useful adjunct to the MobiDB report, since it is not included in that report.

	==Is your query protein in the structural genomics pipeline?==		==Is your query protein in the structural genomics pipeline?==

Eric Martz: /* Has AlphaFold predicted a model? */

2021-11-22T18:46:36Z

Has AlphaFold predicted a model?

← Older revision		Revision as of 18:46, 22 November 2021
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	=== Has AlphaFold predicted a model? ===		=== Has AlphaFold predicted a model? ===
	Empirical models are the most reliable, but if none are available, [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''~~RobeTTaFold~~'' as the method. With any of these methods, download the predicted [[PDB file]] and then upload it to [http://firstglance.jmol.org FirstGlance in Jmol] for exploration and analysis. FirstGlance automatically colors predicted models by reliability.		Empirical models are the most reliable, but if none are available, [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RoseTTaFold'' as the method. With any of these methods, download the predicted [[PDB file]] and then upload it to [http://firstglance.jmol.org FirstGlance in Jmol] for exploration and analysis. FirstGlance automatically colors predicted models by reliability.

	=== Is there an empirical model? ===		=== Is there an empirical model? ===

Eric Martz: /* Has AlphaFold predicted a model? */

2021-11-22T18:44:47Z

Has AlphaFold predicted a model?

← Older revision		Revision as of 18:44, 22 November 2021
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	=== Has AlphaFold predicted a model? ===		=== Has AlphaFold predicted a model? ===
	Empirical models are the most reliable, but if none are available, [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RobeTTaFold'' as the method.		Empirical models are the most reliable, but if none are available, [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RobeTTaFold'' as the method. With any of these methods, download the predicted [[PDB file]] and then upload it to [http://firstglance.jmol.org FirstGlance in Jmol] for exploration and analysis. FirstGlance automatically colors predicted models by reliability.

	=== Is there an empirical model? ===		=== Is there an empirical model? ===

Eric Martz: /* Has AlphaFold predicted a model? */

2021-11-22T18:42:26Z

Has AlphaFold predicted a model?

← Older revision		Revision as of 18:42, 22 November 2021
Line 25:		Line 25:

	=== Has AlphaFold predicted a model? ===		=== Has AlphaFold predicted a model? ===
	Empirical models are the most reliable, but [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RobeTTaFold'' as the method.		Empirical models are the most reliable, but if none are available, [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RobeTTaFold'' as the method.

	=== Is there an empirical model? ===		=== Is there an empirical model? ===

Eric Martz: /* Has AlphaFold predicted a model? */

2021-11-22T18:41:45Z

Has AlphaFold predicted a model?

← Older revision		Revision as of 18:41, 22 November 2021
Line 25:		Line 25:

	=== Has AlphaFold predicted a model? ===		=== Has AlphaFold predicted a model? ===
	Empirical models are the most reliable, but [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RobeTTaFold'' as the method.		Empirical models are the most reliable, but [[AlphaFold]] has an impressive track record of correctly predicting structures from sequence. Check the [http://alphafold.ebi.ac.uk AlphaFold Database] for a model of your protein of interest. You can also submit a sequence and get a prediction: [[How to predict structures with AlphaFold]]. Another model prediction service with a good track record is [http://robetta.bakerlab.org RoseTTaFold]. Submit your sequence there, making sure to check ''RobeTTaFold'' as the method.

	=== Is there an empirical model? ===		=== Is there an empirical model? ===

Eric Martz: /* Do you need a homology model? */

2021-08-29T16:41:21Z

Do you need a homology model?

← Older revision		Revision as of 16:41, 29 August 2021
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	You don’t need a homology model if the amino acid sequence of interest (the query sequence) already has an empirically determined 3D structure. Structures determined empirically, by X-ray crystallography or (much less often) by solution NMR or cryo-EM, will almost always be more accurate than a homology model.		You don’t need a homology model if the amino acid sequence of interest (the query sequence) already has an empirically determined 3D structure. Structures determined empirically, by X-ray crystallography or (much less often) by solution NMR or cryo-EM, will almost always be more accurate than a homology model.

	If [[AlphaFold]] has predicted a model for your amino acid sequence of interest, it will often be more accurate than a homology model.		If [[AlphaFold]] has predicted a model for your amino acid sequence of interest, it will often be more accurate than a homology model, and in most cases, a homology model won't be possible due to lack of a suitable template.

	=== Has AlphaFold predicted a model? ===		=== Has AlphaFold predicted a model? ===

Eric Martz: /* Do you need a homology model? */

2021-08-29T16:40:49Z

Do you need a homology model?

← Older revision		Revision as of 16:40, 29 August 2021
Line 21:		Line 21:

	You don’t need a homology model if the amino acid sequence of interest (the query sequence) already has an empirically determined 3D structure. Structures determined empirically, by X-ray crystallography or (much less often) by solution NMR or cryo-EM, will almost always be more accurate than a homology model.		You don’t need a homology model if the amino acid sequence of interest (the query sequence) already has an empirically determined 3D structure. Structures determined empirically, by X-ray crystallography or (much less often) by solution NMR or cryo-EM, will almost always be more accurate than a homology model.

			If [[AlphaFold]] has predicted a model for your amino acid sequence of interest, it will often be more accurate than a homology model.

	=== Has AlphaFold predicted a model? ===		=== Has AlphaFold predicted a model? ===