add new benchmark datasets

.gitattributes

@@ -82,3 +82,9 @@ bindingdb-kd-filtered.parquet filter=lfs diff=lfs merge=lfs -text
 test.parquet filter=lfs diff=lfs merge=lfs -text
 train.parquet filter=lfs diff=lfs merge=lfs -text
 val.parquet filter=lfs diff=lfs merge=lfs -text
+pdbbind_2013_core.parquet filter=lfs diff=lfs merge=lfs -text
+test_1000_drugs.parquet filter=lfs diff=lfs merge=lfs -text
+test_25_targets_40_percent_similarity.parquet filter=lfs diff=lfs merge=lfs -text
+test_25_targets_60_percent_similarity.parquet filter=lfs diff=lfs merge=lfs -text
+test_25_targets_80_percent_similarity.parquet filter=lfs diff=lfs merge=lfs -text
+pdbbind-2020-general.parquet filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -1,3 +1,6 @@
 env/
 .DS_Store
-affinity-data-combined.parquet
+affinity-data-combined.parquet
+protein_average_similarities.csv
+protein_maximum_similarities.csv
+protein_similarity_matrix.pkl

README.md

@@ -10,10 +10,6 @@ configs:
   data_files:
   - split: train
     path: "train.parquet"
-  - split: test
-    path: "test.parquet"
-  - split: validation
-    path: "val.parquet"
   - split: "combined"
     path: 
       - "train.parquet"
@@ -25,10 +21,12 @@ configs:
     path: "davis-filtered.parquet"
   - split: kiba
     path: "kiba.parquet"
-  - split: pdbbind_2020_combined
-    path: "pdbbind-2020-combined.parquet"
+  - split: pdbbind_2020_general
+    path: "pdbbind-2020-general.parquet"
   - split: pdbbind_2020_refined
     path: "pdbbind-2020-refined.parquet"
+  - split: pdbbind_2013_core
+    path: "pdbbind-2013-core.parquet"
   - split: bindingdb_ic50
     path: "bindingdb-ic50.parquet"
   - split: bindingdb_ki
@@ -39,6 +37,14 @@ configs:
     path: "bindingdb-kd.parquet"
   - split: glaser
     path: "glaser.parquet"
+  - split: drug_screen_test
+    path: "test_1000_drugs.parquet"
+  - split: test_25_targets_40_percent_similarity
+    path: "test_25_targets_40_percent_similarity.parquet"
+  - split: test_25_targets_60_percent_similarity
+    path: "test_25_targets_60_percent_similarity.parquet"
+  - split: test_25_targets_80_percent_similarity
+    path: "test_25_targets_80_percent_similarity.parquet"
 ---
 
 # Binding Affinity Dataset
@@ -47,16 +53,20 @@ configs:
 
 This dataset is a comprehensive collection of protein-ligand binding affinity data, compiled from multiple sources. The dataset is structured with multiple splits, each corresponding to a specific source:
 
-- BindingDB IC50 Split
-- BindingDB Kd Split
-- BindingDB Kd Filtered Split
-- BindingDB Ki Split
-- Davis Split
-- Davis Filtered Split
-- KIBA Split
-- PDBBind 2020 Combined Split
-- PDBBind 2020 Refined Split
-- Glaser Split
+- train split
+- test split
+- validation split
+- combined split
+- davis split
+- davis filtered split
+- kiba split
+- pdbbind 2020 combined split
+- pdbbind 2020 refined split
+- bindingdb ic50 split
+- bindingdb kd split
+- bindingdb kd filtered split
+- bindingdb ki split
+- glaser split
 
 In addition to these source-specific splits, a main training split is provided that combines and aggregates data from all these sources.
 
@@ -104,4 +114,4 @@ The training split is a comprehensive aggregation of multiple molecular binding
 | `neg_log10_affinityM` | Negative logarithm (base 10) of the affinity in molar concentration |
 | `affinity_norm` | Normalized binding affinity |
 | `affinity_mean` | Mean binding affinity for duplicate protein-ligand pairs |
-| `affinity_std` | Standard deviation of binding affinity for duplicate protein-ligand pairs |
+| `affinity_std` | Standard deviation of binding affinity for duplicate protein-ligand pairs |œ

pdbbind-2020-combined.parquet → pdbbind-2013-core.parquet

@@ -1,3 +1,3 @@
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+size 65340

pdbbind-2020-general.parquet

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test_1000_drugs.parquet

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test_25_targets_40_percent_similarity.parquet

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+size 123463

test_25_targets_60_percent_similarity.parquet

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+size 39948

test_25_targets_80_percent_similarity.parquet

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