From 8d9a67abc6daa03de7c6773cfa5558c33621fd4b Mon Sep 17 00:00:00 2001
From: Zeming Lin <zlin@biohub.org>
Date: Wed, 27 May 2026 17:38:49 +0000
Subject: [PATCH] Fix Biohub Platform SDK snippets (ESMC + ESMFold2) and use
 carbonic anhydrase II

---
 README.md                         | 33 +++++++++++++++++++++++--------
 cookbook/tutorials/esmfold2.ipynb |  3 +--
 2 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 8972045..9289487 100644
--- a/README.md
+++ b/README.md
@@ -110,14 +110,24 @@ Then import the necessary libraries and instantiate your desired model.
 
 ```py
 from esm.sdk import esmc_client
-
+from esm.sdk.api import ESMProtein, LogitsConfig
+
+# Human carbonic anhydrase II (PDB 2CBA)
+protein = ESMProtein(
+    sequence=(
+        "MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDD"
+        "SQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVL"
+        "GIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEP"
+        "ISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK"
+    )
+)
 model = esmc_client(
     model="esmc-600m-2024-12", url="https://biohub.ai", token="<your API token>"
 )
 
 protein_tensor = model.encode(protein)
 logits_output = model.logits(
-  protein_tensor, LogitsConfig(sequence=True, return_embeddings=True)
+    protein_tensor, LogitsConfig(sequence=True, return_embeddings=True)
 )
 
 print(logits_output.logits, logits_output.embeddings)
@@ -234,7 +244,8 @@ Import the necessary libraries.
 
 ```py
 from esm.sdk.forge import SequenceStructureForgeInferenceClient
-from esm.sdk.api import ESMProtein, ESMProteinError, LogitsConfig, LogitsOutput
+from esm.sdk.api import FoldingConfig
+from esm.utils.structure.input_builder import ProteinInput, StructurePredictionInput
 ```
 
 Call the inference client with the selected model of choice and replace <your API token> with your token name.
@@ -242,13 +253,19 @@ Call the inference client with the selected model of choice and replace <your AP
 ```py
 client = SequenceStructureForgeInferenceClient(model="esmfold2-fast-2026-05", url="https://biohub.ai", token="<your API token>")
 
-gfp_sequence = "MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYK"
-gfp_input = input_builder.StructurePredictionInput(
-    sequences=[gfp_sequence]
+# Human carbonic anhydrase II (PDB 2CBA)
+ca2_sequence = (
+    "MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDD"
+    "SQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVL"
+    "GIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEP"
+    "ISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK"
+)
+ca2_input = StructurePredictionInput(
+    sequences=[ProteinInput(id="A", sequence=ca2_sequence)]
 )
 
-config = FoldingConfig(num_loops=3, num_sampling_steps=32, seed=0)
-result = client.fold_all_atom(gfp_input, config=config)
+config = FoldingConfig(num_loops=3, num_sampling_steps=32)
+result = client.fold_all_atom(ca2_input, config=config)
 
 with open("result.cif", "w") as f:
     f.write(result.complex.to_mmcif())
diff --git a/cookbook/tutorials/esmfold2.ipynb b/cookbook/tutorials/esmfold2.ipynb
index ccb382e..f564d87 100644
--- a/cookbook/tutorials/esmfold2.ipynb
+++ b/cookbook/tutorials/esmfold2.ipynb
@@ -267,7 +267,6 @@
     "\n",
     "* **num_sampling_steps**: Number of diffusion sampling steps. Higher values produce more accurate structures but take longer (typical range: 200-400).\n",
     "\n",
-    "* **seed**: Random seed for reproducibility. Using the same seed with identical inputs will produce the same structure.\n",
     "\n",
     "We use a moderate number of loops (3) and sampling steps (32) to balance accuracy and runtime for this example. For more accurate results, especially when modeling flexible ligands or uncertain binding modes, you can increase num_loops and num_sampling_steps at the cost of longer runtimes."
    ]
@@ -278,7 +277,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "config = FoldingConfig(num_loops=3, num_sampling_steps=32, seed=2, include_pae=True)"
+    "config = FoldingConfig(num_loops=3, num_sampling_steps=32, include_pae=True)"
    ]
   },
   {