Practical Guide to Homology Modeling - Revision history

Jaime Prilusky at 17:54, 13 February 2022

Jaime Prilusky — Sun, 13 Feb 2022 17:54:39 GMT

←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? */

Eric Martz — Mon, 22 Nov 2021 18:46:36 GMT

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? */

Eric Martz — Mon, 22 Nov 2021 18:44:47 GMT

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? */

Eric Martz — Mon, 22 Nov 2021 18:42:26 GMT

Has AlphaFold predicted a model?

←Older revision		Revision as of 18:42, 22 November 2021
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	=== 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? */

Eric Martz — Mon, 22 Nov 2021 18:41:45 GMT

Has AlphaFold predicted a model?

←Older revision		Revision as of 18:41, 22 November 2021
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	=== 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? */

Eric Martz — Sun, 29 Aug 2021 16:41:21 GMT

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? */

Eric Martz — Sun, 29 Aug 2021 16:40:49 GMT

Do you need a homology model?

←Older revision		Revision as of 16:40, 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.

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

Eric Martz: /* Has AlphaFold Predicted a Model? */

Eric Martz — Sun, 29 Aug 2021 16:22:44 GMT

Has AlphaFold Predicted a Model?

←Older revision		Revision as of 16:22, 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.

-	=== Has AlphaFold ~~Predicted~~ a ~~Model~~? ===	+	=== Has AlphaFold predicted a model? ===
-	[[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. 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: /* Is there an empirical model? */

Eric Martz — Sat, 28 Aug 2021 23:14:39 GMT

Is there an empirical model?

←Older revision		Revision as of 23:14, 28 August 2021
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	=== Is there an empirical model? ===		=== Is there an empirical model? ===

-	All published, empirically-determined, atomic-resolution, macromolecular 3D structures are available in the [[World Wide Protein Data Bank]].	+	[[Empirical models\|Empirically-determined]] models are usually the most reliable. All published, empirically-determined, atomic-resolution, macromolecular 3D structures are available in the [[World Wide Protein Data Bank]].

	Each model in the PDB has a unique 4-character identification code ([[PDB ID]]) that begins with a numeral, and has letters or numerals for the last 3 characters . Examples are 1d66, 4mdh, 9ins.		Each model in the PDB has a unique 4-character identification code ([[PDB ID]]) that begins with a numeral, and has letters or numerals for the last 3 characters . Examples are 1d66, 4mdh, 9ins.

Eric Martz: /* Is there an empirical model? */

Eric Martz — Sat, 28 Aug 2021 23:13:10 GMT

Is there an empirical model?

←Older revision		Revision as of 23:13, 28 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.
		+
		+	=== Has AlphaFold Predicted a Model? ===
		+	[[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.

	=== Is there an empirical model? ===		=== Is there an empirical model? ===
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	Each model in the PDB has a unique 4-character identification code ([[PDB ID]]) that begins with a numeral, and has letters or numerals for the last 3 characters . Examples are 1d66, 4mdh, 9ins.		Each model in the PDB has a unique 4-character identification code ([[PDB ID]]) that begins with a numeral, and has letters or numerals for the last 3 characters . Examples are 1d66, 4mdh, 9ins.

-	Here are two methods for finding out if your query amino acid sequence, or parts of it, have empirically-determined 3D structures in the PDB.	+	Here are two methods for finding out if your query amino acid sequence, or parts of it, have [[Empirical models\|empirically-determined 3D structures]] in the PDB.

	==== Simple search for empirical models (via PIR) ====		==== Simple search for empirical models (via PIR) ====