How to predict structures with AlphaFold: Difference between revisions
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Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
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Don't worry about any of the options not specifically mentioned below. Leave them at their default settings. | Don't worry about any of the options not specifically mentioned below. Leave them at their default settings. | ||
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1. Obtain the sequence of the protein of interest, e.g. at [http://uniprot.org UniProt]. | 1. Obtain the sequence of the protein of interest, e.g. at [http://uniprot.org UniProt]. Copy only the sequence, excluding the FASTA header line that begins with ">". | ||
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2. Login with a google account at [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb AlphaFold2_advanced]. You can register for a free gmail account to use for login. | 2. Login with a google account at [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb AlphaFold2_advanced]. You can register for a free gmail account to use for login. | ||
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3. Paste in your sequence, making sure to completely replace the default sequence: | 3. Paste in your sequence, making sure to completely replace the default sequence: | ||
<br>[[Image:AF2Adv-seq1.png|400px]]<br> | <br> | ||
[[Image:AF2Adv-seq1.png|400px]] | |||
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This input slot can accept sequences >1,000 amino acids, even though it is only one line. Sequence lengths of ~1,000 amino acids, or longer, may cause the Colab to fail, but can be predicted by submitting in two halves.<ref name="halves">I had one sequence of length ~1,300. After it failed, I submitted it as two halves with a substantial overlap (~350 residues). The middle overlap of ~200 residues of the predicted structures superposed very closely with [[DeepView]]. I trimmed off the ends that superposed poorly, and superposed the two halves via the mid-overlap. By inspection, I chose pair of alpha carbons near the middle where the alpha carbon positions were nearly identical. I trimmed each half to this position, and "ligated" the two halves by combining the superposed half PDB files with a text editor. For further details, contact [[User:Eric_Martz]].</ref> | This input slot can accept sequences >1,000 amino acids, even though it is only one line. Sequence lengths of ~1,000 amino acids, or longer, may cause the Colab to fail, but can be predicted by submitting in two halves.<ref name="halves">I had one sequence of length ~1,300. After it failed, I submitted it as two halves with a substantial overlap (~350 residues). The middle overlap of ~200 residues of the predicted structures superposed very closely with [[DeepView]]. I trimmed off the ends that superposed poorly, and superposed the two halves via the mid-overlap. By inspection, I chose pair of alpha carbons near the middle where the alpha carbon positions were nearly identical. I trimmed each half to this position, and "ligated" the two halves by combining the superposed half PDB files with a text editor. For further details, contact [[User:Eric_Martz]].</ref> | ||
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