How to predict structures with AlphaFold - Revision history

Eric Martz at 18:23, 27 April 2026

2026-04-27T18:23:30Z

← Older revision		Revision as of 18:23, 27 April 2026
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	[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of ~~uploaded~~ AlphaFold or RoseTTAFold models by estimated confidence [[pLDDT]] ('''{{Font color\|blue\|blue for high confidence}}, {{Font color\|red\|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.		[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of AlphaFold or RoseTTAFold models by estimated confidence [[pLDDT]] ('''{{Font color\|blue\|blue for high confidence}}, {{Font color\|red\|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.

	*[[iCn3D]] automatically colors AlphaFold2 Database models loaded from their UniProt IDs. For AlphaFold files opened from your computer, use pLDDT on the pull-down Color menu.		*[[iCn3D]] automatically colors AlphaFold2 Database models loaded from their UniProt IDs. For AlphaFold files opened from your computer, use pLDDT on the pull-down Color menu.
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	[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities].		[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities].

	~~You can easily~~ visualize		When using [http://FirstGlance.jmol.org FirstGlance], it is easy to visualize
	* Estimated confidence/pLDDT by touching an atom		* Estimated confidence/pLDDT by touching an atom
	* '''Average confidence/pLDDT''' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models\|a specified sequence range]].		* '''Average confidence/pLDDT''' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models\|a specified sequence range]].

Eric Martz at 18:19, 27 April 2026

2026-04-27T18:19:42Z

← Older revision		Revision as of 18:19, 27 April 2026
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	* 2024<ref name="af3" />: [https://alphafoldserver.com AlphaFoldServer.Com]. Using AlphaFold3, predicts homo- and hetro-multimers involving protein, DNA, RNA, ligands, and modified residues. Straightforward to use; Guide and FAQ provided. Predictions are templated without user control (see FAQ). Free for non-commercial use -- see [https://alphafoldserver.com/terms Terms of Service] and [https://alphafoldserver.com/output-terms Output Terms of Use]. From the DeepMind team<ref name="af3" />.		* 2024<ref name="af3" />: [https://alphafoldserver.com AlphaFoldServer.Com]. Using AlphaFold3, predicts homo- and hetro-multimers involving protein, DNA, RNA, ligands, and modified residues. Straightforward to use; Guide and FAQ provided. Predictions are templated without user control (see FAQ). Free for non-commercial use -- see [https://alphafoldserver.com/terms Terms of Service] and [https://alphafoldserver.com/output-terms Output Terms of Use]. From the DeepMind team<ref name="af3" />.
	**If you get <font color="red"><b>Invalid character</b></font> after pasting in your sequence, try removing the breaks between lines.		**If you get <font color="red"><b>Invalid character</b></font> after pasting in your sequence, try removing the breaks between lines.
	**Predicted models are in [[Mmcif format\|mmCIF format]] only. ~~To convert to [[PDB format]] for use~~ in [[FirstGlance in Jmol~~\|FirstGlance~~]~~] (which colors~~ by confidence/pLDDT ~~automatically), see~~ [[Converting AlphaFold3 CIF to PDB]].		**Predicted models are in [[Mmcif format\|mmCIF format]] only. When visualized in [http://firstglance.jmol.org FirstGlance in Jmol], coloring by confidence/pLDDT is automatic. [[Converting AlphaFold3 CIF to PDB\|More information about .cif and FirstGlance]].
	**To easily obtain average [[pLDDT]] (predicted confidence) for a range of residues, see [[FirstGlance/How to get average pLDDT from AlphaFold models]].		**To easily obtain average [[pLDDT]] (predicted confidence) for a range of residues, see [[FirstGlance/How to get average pLDDT from AlphaFold models]].
	**Chain ID assignments differ from those of empirical wwPDB files: see [[Chains_and_Chain_IDs#AlphaFold3_Chain_IDs\|AlphaFold3 Chain IDs]].		**Chain ID assignments differ from those of empirical wwPDB files: see [[Chains_and_Chain_IDs#AlphaFold3_Chain_IDs\|AlphaFold3 Chain IDs]].

Eric Martz: /* Prediction Servers */

2025-05-19T06:31:23Z

Prediction Servers

← Older revision		Revision as of 06:31, 19 May 2025
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	**Predicted models are in [[Mmcif format\|mmCIF format]] only. To convert to [[PDB format]] for use in [[FirstGlance in Jmol\|FirstGlance]] (which colors by confidence/pLDDT automatically), see [[Converting AlphaFold3 CIF to PDB]].		**Predicted models are in [[Mmcif format\|mmCIF format]] only. To convert to [[PDB format]] for use in [[FirstGlance in Jmol\|FirstGlance]] (which colors by confidence/pLDDT automatically), see [[Converting AlphaFold3 CIF to PDB]].
	**To easily obtain average [[pLDDT]] (predicted confidence) for a range of residues, see [[FirstGlance/How to get average pLDDT from AlphaFold models]].		**To easily obtain average [[pLDDT]] (predicted confidence) for a range of residues, see [[FirstGlance/How to get average pLDDT from AlphaFold models]].
			**Chain ID assignments differ from those of empirical wwPDB files: see [[Chains_and_Chain_IDs#AlphaFold3_Chain_IDs\|AlphaFold3 Chain IDs]].
	**See also [[#Visualizing Predicted Structures]] and [[User:Eric Martz/AlphaFold3 case studies\|AlphaFold3 case studies]].		**See also [[#Visualizing Predicted Structures]] and [[User:Eric Martz/AlphaFold3 case studies\|AlphaFold3 case studies]].

Eric Martz: /* Prediction Servers */

2025-05-17T20:52:55Z

Prediction Servers

← Older revision		Revision as of 20:52, 17 May 2025
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	* 2024<ref name="rfaa">PMID: 38452047</ref>: RosettaFold All-Atom (RFAA) predicts multimers of protein and nucleic acids with ligands. From the Baker team<ref name="rfaa" />. [https://neurosnap.ai/service/RoseTTAFold%20All-Atom A free server limited to very small numbers of jobs is available from Neurosnap].		* 2024<ref name="rfaa">PMID: 38452047</ref>: RosettaFold All-Atom (RFAA) predicts multimers of protein and nucleic acids with ligands. From the Baker team<ref name="rfaa" />. [https://neurosnap.ai/service/RoseTTAFold%20All-Atom A free server limited to very small numbers of jobs is available from Neurosnap].

	* 2024 update? [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ColabFold AlphaFold2 and AlphaFold-multimer] predicts multiple chain complexes. Easy to use. From ~~Mirdata~~ ''et al.''<ref name="colabfold" />		* 2024 update? [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ColabFold AlphaFold2 and AlphaFold-multimer] predicts multiple chain complexes. Easy to use. From Mirdita ''et al.''<ref name="colabfold" />

	* 2024<ref name="combfold">PMID: 38326495</ref>: [https://neurosnap.ai/service/CombFold CombFold] predicts the structures of large protein complexes from subunit sequences using AlphaFold Multimer paired with a combinatorial method to assemble subunits. From Shor and Schneidman-Duhovny<ref name="combfold" />.		* 2024<ref name="combfold">PMID: 38326495</ref>: [https://neurosnap.ai/service/CombFold CombFold] predicts the structures of large protein complexes from subunit sequences using AlphaFold Multimer paired with a combinatorial method to assemble subunits. From Shor and Schneidman-Duhovny<ref name="combfold" />.

Eric Martz: /* Prediction Servers */

2025-05-17T20:52:26Z

Prediction Servers

← Older revision		Revision as of 20:52, 17 May 2025
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	* 2024<ref name="rfaa">PMID: 38452047</ref>: RosettaFold All-Atom (RFAA) predicts multimers of protein and nucleic acids with ligands. From the Baker team<ref name="rfaa" />. [https://neurosnap.ai/service/RoseTTAFold%20All-Atom A free server limited to very small numbers of jobs is available from Neurosnap].		* 2024<ref name="rfaa">PMID: 38452047</ref>: RosettaFold All-Atom (RFAA) predicts multimers of protein and nucleic acids with ligands. From the Baker team<ref name="rfaa" />. [https://neurosnap.ai/service/RoseTTAFold%20All-Atom A free server limited to very small numbers of jobs is available from Neurosnap].

	* 2024 update? [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ColabFold AlphaFold2 and AlphaFold-multimer] predicts multiple chain complexes. Easy to use.		* 2024 update? [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ColabFold AlphaFold2 and AlphaFold-multimer] predicts multiple chain complexes. Easy to use. From Mirdata ''et al.''<ref name="colabfold" />

	* 2024<ref name="combfold">PMID: 38326495</ref>: [https://neurosnap.ai/service/CombFold CombFold] predicts the structures of large protein complexes from subunit sequences using AlphaFold Multimer paired with a combinatorial method to assemble subunits. From Shor and Schneidman-Duhovny<ref name="combfold" />.		* 2024<ref name="combfold">PMID: 38326495</ref>: [https://neurosnap.ai/service/CombFold CombFold] predicts the structures of large protein complexes from subunit sequences using AlphaFold Multimer paired with a combinatorial method to assemble subunits. From Shor and Schneidman-Duhovny<ref name="combfold" />.

Eric Martz: /* Prediction Servers */

2025-05-17T20:49:50Z

Prediction Servers

← Older revision		Revision as of 20:49, 17 May 2025
Line 24:		Line 24:
	* 2024<ref name="rfaa">PMID: 38452047</ref>: RosettaFold All-Atom (RFAA) predicts multimers of protein and nucleic acids with ligands. From the Baker team<ref name="rfaa" />. [https://neurosnap.ai/service/RoseTTAFold%20All-Atom A free server limited to very small numbers of jobs is available from Neurosnap].		* 2024<ref name="rfaa">PMID: 38452047</ref>: RosettaFold All-Atom (RFAA) predicts multimers of protein and nucleic acids with ligands. From the Baker team<ref name="rfaa" />. [https://neurosnap.ai/service/RoseTTAFold%20All-Atom A free server limited to very small numbers of jobs is available from Neurosnap].

	* 2024<ref name="combfold">PMID: 38326495</ref>: [https://neurosnap.ai/service/CombFold CombFold] predicts the structures of large protein complexes from subunit sequences using AlphaFold Multimer paired with a ~~cominatorial~~ method to assemble subunits. From Shor and Schneidman-Duhovny<ref name="combfold" />.		* 2024 update? [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ColabFold AlphaFold2 and AlphaFold-multimer] predicts multiple chain complexes. Easy to use.

			* 2024<ref name="combfold">PMID: 38326495</ref>: [https://neurosnap.ai/service/CombFold CombFold] predicts the structures of large protein complexes from subunit sequences using AlphaFold Multimer paired with a combinatorial method to assemble subunits. From Shor and Schneidman-Duhovny<ref name="combfold" />.

	* 2022<ref name="colabfold">PMID: 35637307</ref>: [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb ColabFold AlphaFold2_advanced]. Predicts homo- and hetero-multimers using methods from the Steinegger/Mirdita team<ref name="colabfold" /><ref name="colabfold2024">PMID: 39402428</ref>, before AlphaFold-multimer<ref name="afmultimer">[https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1.full Protein complex prediction with AlphaFold-Multimer], Preprint, Evans et al. 2021.</ref> was available. Does NOT use templates. [https://www.ebi.ac.uk/training/online/courses/alphafold/accessing-and-predicting-protein-structures-with-alphafold/predicting-protein-structures-with-colabfold-and-alphafold-colab/ See Instructions from EMBL-EBI].		* 2022<ref name="colabfold">PMID: 35637307</ref>: [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb ColabFold AlphaFold2_advanced]. Predicts homo- and hetero-multimers using methods from the Steinegger/Mirdita team<ref name="colabfold" /><ref name="colabfold2024">PMID: 39402428</ref>, before AlphaFold-multimer<ref name="afmultimer">[https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1.full Protein complex prediction with AlphaFold-Multimer], Preprint, Evans et al. 2021.</ref> was available. Does NOT use templates. [https://www.ebi.ac.uk/training/online/courses/alphafold/accessing-and-predicting-protein-structures-with-alphafold/predicting-protein-structures-with-colabfold-and-alphafold-colab/ See Instructions from EMBL-EBI].

Eric Martz: /* See Also */

2024-11-25T21:28:55Z

Eric Martz: /* Visualizing Predicted Structures */

2024-11-13T19:07:44Z

Visualizing Predicted Structures

← Older revision		Revision as of 19:07, 13 November 2024
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	You can easily visualize		You can easily visualize
	* Estimated confidence/pLDDT by touching an atom		* Estimated confidence/pLDDT by touching an atom
	* '''Average confidence/pLDDT'' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models\|a specified sequence range]].		* '''Average confidence/pLDDT''' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models\|a specified sequence range]].
	* Secondary structure (Views tab)		* Secondary structure (Views tab)
	* Distribution of hydrophobic vs. polar residues (Views tab: integral membrane proteins will have large hydrophobic surfaces while soluble proteins will have hydrophobic cores revealed by the ''Slab'' button)		* Distribution of hydrophobic vs. polar residues (Views tab: integral membrane proteins will have large hydrophobic surfaces while soluble proteins will have hydrophobic cores revealed by the ''Slab'' button)

Eric Martz: /* Visualizing Predicted Structures */

2024-11-13T19:07:29Z

Visualizing Predicted Structures

← Older revision		Revision as of 19:07, 13 November 2024
Line 55:		Line 55:
	You can easily visualize		You can easily visualize
	* Estimated confidence/pLDDT by touching an atom		* Estimated confidence/pLDDT by touching an atom
	* Average confidence/pLDDT for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models\|a specified sequence range]].		* '''Average confidence/pLDDT'' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models\|a specified sequence range]].
	* Secondary structure (Views tab)		* Secondary structure (Views tab)
	* Distribution of hydrophobic vs. polar residues (Views tab: integral membrane proteins will have large hydrophobic surfaces while soluble proteins will have hydrophobic cores revealed by the ''Slab'' button)		* Distribution of hydrophobic vs. polar residues (Views tab: integral membrane proteins will have large hydrophobic surfaces while soluble proteins will have hydrophobic cores revealed by the ''Slab'' button)

Eric Martz: /* Visualizing Predicted Structures */

2024-11-13T19:06:46Z

Visualizing Predicted Structures

← Older revision		Revision as of 19:06, 13 November 2024
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	[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of uploaded AlphaFold or RoseTTAFold models by estimated confidence [[pLDDT]] ('''{{Font color\|blue\|blue for high confidence}}, {{Font color\|red\|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.		[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of uploaded AlphaFold or RoseTTAFold models by estimated confidence [[pLDDT]] ('''{{Font color\|blue\|blue for high confidence}}, {{Font color\|red\|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.

	[[iCn3D]] automatically colors AlphaFold2 Database models loaded from their UniProt IDs. For AlphaFold files opened from your computer, use pLDDT on the pull-down Color menu.		*[[iCn3D]] automatically colors AlphaFold2 Database models loaded from their UniProt IDs. For AlphaFold files opened from your computer, use pLDDT on the pull-down Color menu.

	[[PyMOL]] and [[ChimeraX]] have no built-in confidence/pLDDT color scheme. Their rainbow/spectrum color schemes for temperature/B-factor color confidence/pLDDT with the AlphaFold color scheme inverted.		*[[PyMOL]] and [[ChimeraX]] have no built-in confidence/pLDDT color scheme. Their rainbow/spectrum color schemes for temperature/B-factor color confidence/pLDDT with the AlphaFold color scheme inverted.

	[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities].		[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities].

← Older revision		Revision as of 21:28, 25 November 2024
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	==See Also==		==See Also==
	*[[AlphaFold/Index]], a list of pages in Proteopedia about Alphafold.		*[[AlphaFold/Index]], a list of pages in Proteopedia about Alphafold.
			*[[User:Eric Martz/AlphaFold3 case studies\|AlphaFold3 case studies]] includes a case that AlphaFold3 cannot predict.
	*[[How To Find A Structure]]		*[[How To Find A Structure]]
	*[[Missing residues and incomplete sidechains]]		*[[Missing residues and incomplete sidechains]]