"Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ > _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n",
"\n",
"Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)."
"Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)."
]
]
},
},
{
"cell_type": "code",
"metadata": {
"id": "rowN0bVYLe9n",
"cellView": "form"
},
"source": [
"#@markdown ### Enter the amino acid sequence to fold ⬇️\n",
"aatypes = set('ACDEFGHIKLMNPQRSTVWY') # 20 standard aatypes\n",
"if not set(sequence).issubset(aatypes):\n",
" raise Exception(f'Input sequence contains non-amino acid letters: {set(sequence) - aatypes}. AlphaFold only supports 20 standard amino acids as inputs.')\n",
"if len(sequence) < MIN_SEQUENCE_LENGTH:\n",
" raise Exception(f'Input sequence is too short: {len(sequence)} amino acids, while the minimum is {MIN_SEQUENCE_LENGTH}')\n",
"if len(sequence) > MAX_SEQUENCE_LENGTH:\n",
" raise Exception(f'Input sequence is too long: {len(sequence)} amino acids, while the maximum is {MAX_SEQUENCE_LENGTH}. Please use the full AlphaFold system for long sequences.')"
],
"execution_count": null,
"outputs": []
},
{
{
"cell_type": "code",
"cell_type": "code",
"metadata": {
"metadata": {
...
@@ -298,12 +310,6 @@
...
@@ -298,12 +310,6 @@
"#@markdown you’ll see how well each residue is covered by similar \n",
"#@markdown you’ll see how well each residue is covered by similar \n",
