Add more fixes

Author: ebetica

.pre-commit-config.yaml

@@ -32,7 +32,7 @@ repos:
       types: [python]
       pass_filenames: true # For speed, we only check the files that are changed
       # Modal-app tutorial: deps (modal, abnumber) and dynamic decorators aren't resolvable in the lint env.
-      exclude: ^cookbook/tutorials/esmfold2_esmc_binder_design\.py$
+      exclude: ^cookbook/tutorials/binder_design\.py$
 - repo: https://github.com/gitleaks/gitleaks
   rev: v8.24.2
   hooks:

README.md

@@ -25,7 +25,7 @@ We are releasing a world model for protein biology: a scientific engine for pred
 </div>
 
 
-ESMFold2 is validated in the lab across five therapeutic targets. Inversion of ESMFold2 enables generation of de novo minibinders and antibody-derived scFvs with high hit rates, nanomolar affinities, target specificity, and functional activity. We've released the full protocol from target sequence to ranked binder design in this [notebook](https://github.com/Biohub/esm/blob/main/cookbook/tutorials/esmfold2_esmc_binder_design.ipynb). For additional details, please refer to the [preprint](https://biohub.ai/papers/esm_protein.pdf).
+ESMFold2 is validated in the lab across five therapeutic targets. Inversion of ESMFold2 enables generation of de novo minibinders and antibody-derived scFvs with high hit rates, nanomolar affinities, target specificity, and functional activity. We've released the full protocol from target sequence to ranked binder design in this [notebook](https://github.com/Biohub/esm/blob/main/cookbook/tutorials/binder_design.ipynb). For additional details, please refer to the [preprint](https://biohub.ai/papers/esm_protein.pdf).
 
 <div align="center">
   <img src="_assets/esmfold2_binder.png" width="60%"/>

cookbook/tutorials/README.md

@@ -26,7 +26,7 @@ ESMFold2 predicts 3D protein structure from sequence, including DNA/RNA and smal
 | Notebook | Colab Notebook | Description |
 | :---- | :---- | :---- |
 | Folding with ESMFold2 | `esmfold2.ipynb`<br>[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/biohub/esm/blob/main/cookbook/tutorials/esmfold2.ipynb) | Fold proteins in combination with DNA, RNA and small-molecule ligands. |
-| Binder design | `esmfold2_esmc_binder_design.ipynb`<br>[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/biohub/esm/blob/main/cookbook/tutorials/esmfold2_esmc_binder_design.ipynb) | Design antibodies and minibinders with high hit rates. Implements the protocol featured in our paper, which produced binders exhibiting nanomolar affinity, target specificity, and functional activity in laboratory assays. |
+| Binder design | `binder_design.ipynb`<br>[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/biohub/esm/blob/main/cookbook/tutorials/binder_design.ipynb) | Design antibodies and minibinders with high hit rates. Implements the protocol featured in our paper, which produced binders exhibiting nanomolar affinity, target specificity, and functional activity in laboratory assays. |
 
 ## **ESM3**
 

…orials/esmfold2_esmc_binder_design.ipynb cookbook/tutorials/binder_design.ipynbcookbook/tutorials/esmfold2_esmc_binder_design.ipynb renamed to cookbook/tutorials/binder_design.ipynb cookbook/tutorials/esmfold2_esmc_binder_design.ipynb renamed to cookbook/tutorials/binder_design.ipynb

@@ -52,9 +52,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Deploy (or redeploy after changing modal_binder_design.py).\n",
-    "# This only needs to be run a single time, unless code in esmfold2_esmc_binder_design.py changes.\n",
-    "! modal deploy esmfold2_esmc_binder_design.py"
+    "# Deploy (or redeploy after changing binder_design.py).\n",
+    "# This only needs to be run a single time, unless code in binder_design.py changes.\n",
+    "! modal deploy binder_design.py"
    ]
   },
   {
@@ -146,7 +146,7 @@
     "# ---- Option 2: Provide your own sequences. ----\n",
     "# Our pd-l1 sequence crop.\n",
     "pdl1_sequence = \"AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNA\"\n",
-    "# A sample of 'trastuzumab_framework_vhvl' template.  From esmfold2_esmc_binder_design.py::BINDER_PROMPT_FACTORIES.\n",
+    "# A sample of 'trastuzumab_framework_vhvl' template.  From binder_design.py::BINDER_PROMPT_FACTORIES.\n",
     "trastuzumab_framework_vhvl = \"EVQLVESGGGLVQPGGSLRLSCAAS#######YIHWVRQAPGKGLEWVARI#####TRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSR###########WGQGTLVTVSSGGGSGGGSGGGSGGGSDIQMTQSPSSLSASVGDRVTITC###########WYQQKPGKAPKLLIY#######GVPSRFSGSRSGTDFTLTISSLQPEDFATYYC#########FGQGTKVEIK\"\n",
     "future2 = app.design.spawn(\n",
     "    target_sequence=pdl1_sequence,\n",