Practical Guide to Homology Modeling: Difference between revisions
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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) ==== | ||
