How to predict structures with AlphaFold
From Proteopedia
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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 ~200 of the | + | 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> |
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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). | ||
Revision as of 21:05, 17 October 2021
In 2020, the AlphaFold project of Google's DeepMind team demonstrated a major breakthrough in predicting protein structure from sequence. Their success in the blind CASP competition astonished many experts. For an overview, see Theoretical models.
In July, 2021, DeepMind released AlphaFold as open source code. Subsequently, several Colabs became available offering free structure prediction for user-submitted protein sequences. These Google Colabs (collaboratories)[1]. enable users to submit sequences via web browser, executing the code in the Google cloud, using space private to each user, returning predicted structures.
Below are instructions for beginners who wish to predict structures. We recommend the "advanced" Colab by Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger.
Instructions
Don't worry about any of the options not specifically mentioned below. Leave them at their default settings.
1. Obtain the sequence of the protein of interest, e.g. at UniProt.
2. Login at AlphaFold2_advanced. Registration is free.
3. Paste in your sequence, making sure to completely replace the default sequence:
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.[2]
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).
References and Notes
- ↑ Collaboratory FAQ at Google.
- ↑ 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.
