From 961c7afda81a2bc8d8990d539cce25dc5a15dd1f Mon Sep 17 00:00:00 2001 From: Sergey O Date: Sat, 11 Mar 2023 13:30:21 -0500 Subject: [PATCH] fix cyclic hallucination weights --- af/examples/af_cyc_design.ipynb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/af/examples/af_cyc_design.ipynb b/af/examples/af_cyc_design.ipynb index bc0d78a5..f9d9ff9b 100644 --- a/af/examples/af_cyc_design.ipynb +++ b/af/examples/af_cyc_design.ipynb @@ -16,8 +16,13 @@ "id": "OA2k3sAYuiXe" }, "source": [ - "#AfCysDesign (WIP)\n", - "Backprop through AlphaFold for protein design with cyclic support\n" + "#af_cys_design\n", + "\n", + "**Cyclic peptide structure prediction and design using AlphaFold**\n", + "\n", + "Stephen Rettie, Katelyn Campbell, Asim Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank DiMaio, Sergey Ovchinnikov, Gaurav Bhardwaj\n", + "\n", + "doi: https://doi.org/10.1101/2023.02.25.529956\n" ] }, { @@ -197,6 +202,7 @@ "# pre-design with gumbel initialization and softmax activation\n", "af_model.restart(mode=\"gumbel\")\n", "af_model.set_opt(\"con\", binary=True, cutoff=21.6875, num=af_model._len, seqsep=0)\n", + "af_model.set_weights(pae=1, plddt=1, con=0.5)\n", "af_model.design_soft(50)\n", "\n", "# three stage design \n",