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BioinfoMachineLearning · Jan 28, 2025 · e1b0f68 · e1b0f68
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/notebooks/casp15_method_interaction_analysis_plotting.ipynb b/notebooks/casp15_method_interaction_analysis_plotting.ipynb
@@ -77,12 +77,13 @@
     "    \"vina_p2rank\",\n",
     "    \"diffdock\",\n",
     "    \"dynamicbind\",\n",
-    "    \"neuralplexer\",\n",
     "    \"rfaa\",\n",
     "    \"chai-lab_ss\",\n",
     "    \"chai-lab\",\n",
     "    \"alphafold3_ss\",\n",
     "    \"alphafold3\",\n",
+    "    \"neuralplexer3_ss\",\n",
+    "    \"neuralplexer3\",\n",
     "]\n",
     "max_num_repeats_per_method = (\n",
     "    1  # NOTE: Here, to simplify the analysis, we only consider the first run of each method\n",
@@ -103,12 +104,13 @@
     "    \"vina_p2rank\": \"P2Rank-Vina\",\n",
     "    \"diffdock\": \"DiffDock-L\",\n",
     "    \"dynamicbind\": \"DynamicBind\",\n",
-    "    \"neuralplexer\": \"NeuralPLexer\",\n",
     "    \"rfaa\": \"RoseTTAFold-AA\",\n",
     "    \"chai-lab_ss\": \"Chai-1-Single-Seq\",\n",
     "    \"chai-lab\": \"Chai-1\",\n",
     "    \"alphafold3_ss\": \"AF3-Single-Seq\",\n",
     "    \"alphafold3\": \"AF3\",\n",
+    "    \"neuralplexer3_ss\": \"NP3-Single-Seq\",\n",
+    "    \"neuralplexer3\": \"NP3\",\n",
     "}\n",
     "\n",
     "CASP15_ANALYSIS_TARGETS_TO_SKIP = [\n",

diff --git a/notebooks/casp15_method_interaction_analysis_plotting.py b/notebooks/casp15_method_interaction_analysis_plotting.py
@@ -42,12 +42,13 @@
     "vina_p2rank",
     "diffdock",
     "dynamicbind",
-    "neuralplexer",
     "rfaa",
     "chai-lab_ss",
     "chai-lab",
     "alphafold3_ss",
     "alphafold3",
+    "neuralplexer3_ss",
+    "neuralplexer3",
 ]
 max_num_repeats_per_method = (
     1  # NOTE: Here, to simplify the analysis, we only consider the first run of each method
@@ -68,12 +69,13 @@
     "vina_p2rank": "P2Rank-Vina",
     "diffdock": "DiffDock-L",
     "dynamicbind": "DynamicBind",
-    "neuralplexer": "NeuralPLexer",
     "rfaa": "RoseTTAFold-AA",
     "chai-lab_ss": "Chai-1-Single-Seq",
     "chai-lab": "Chai-1",
     "alphafold3_ss": "AF3-Single-Seq",
     "alphafold3": "AF3",
+    "neuralplexer3_ss": "NP3-Single-Seq",
+    "neuralplexer3": "NP3",
 }
 
 CASP15_ANALYSIS_TARGETS_TO_SKIP = [