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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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]]<br> | ||
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 of the predicted structures superposed very closely. 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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4. Enter a jobname in the slot below the sequence slot. The results.zip filename will begin with this jobname (but none of its contents include the jobname). | 4. Enter a jobname in the slot below the sequence slot. The results.zip filename will begin with this jobname (but none of its contents include the jobname). | ||
