update README and colab nb to reflect the new AlphaFold version

README.md

@@ -5,6 +5,10 @@ Python tools for TCR:peptide-MHC modeling and analysis
 Described in the manuscript: "Structure-based prediction of T cell
 receptor:peptide-MHC interactions" by Philip Bradley. bioRXiv link: 
 
+***[NEW 2024-03-06]*** The AlphaFold code was updated to alphafold v2.3.2
+from alphafold repo commit f715f016d875e2fd8515457af2b12277a716b9b0
+The old code can be found in the releases section under v1.0.0
+
 ***[NEW 2024-01-17]*** The [Google colab notebook](tcrdock_colab_pipeline_v1.ipynb) was
 temporarily broken due to an update of the colab GPU libraries (CUDA/CUDNN). I just
 checked in an updated version that should be working again. This is a short-term patch

tcrdock_colab_pipeline_v1.ipynb

@@ -7,7 +7,7 @@
         "colab_type": "text"
       },
       "source": [
-        "<a href=\"https://colab.research.google.com/github/phbradley/TCRdock/blob/af232_update/tcrdock_colab_pipeline_v1_af232.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+        "<a href=\"https://colab.research.google.com/github/phbradley/TCRdock/blob/main/tcrdock_colab_pipeline_v1.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
       ]
     },
     {
@@ -182,7 +182,7 @@
         "  with tqdm.notebook.tqdm(total=100, bar_format=TQDM_BAR_FORMAT) as pbar:\n",
         "    with io.capture_output() as captured:\n",
         "      %shell rm -rf TCRdock\n",
-        "      %shell git clone --branch af232_update {GIT_REPO} TCRdock\n",
+        "      %shell git clone --branch main {GIT_REPO} TCRdock\n",
         "      pbar.update(20)\n",
         "      # Install the required versions of all dependencies.\n",
         "      %shell pip3 install -r ./TCRdock/requirements_colab_af232.txt\n",