Practical Guide to Homology Modeling: Difference between revisions
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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> | ||
<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]]. | |||
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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 == | ||
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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 | 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. | ||
[[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 '' | |||
=== 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 ''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? === | ||
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==== FoldIndex ==== | ==== FoldIndex ==== | ||
The [ | 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?== | ||