Update README.md

README.md

@@ -78,10 +78,10 @@ cd protap
 
 | Config Name | Task Description                                      | Modality       | Split        | File Types                    |
 |-------------|--------------------------------------------------------|----------------|--------------|-------------------------------|
-| `AFP`       | Protein function annotation (GO term prediction)      | Sequence-only  | `test`       | `.csv`                        |
+| `AFP`       | Protein function annotation (GO term prediction)      | Seq + Struct   | `test`       | `.csv`,`json`                        |
 | `PCSP`      | Cleavage site prediction (enzyme-substrate pairs)     | Seq + Struct   | `train/test` | `.pkl`                        |
-| `PLI_DAVIS` | Protein–ligand binding affinity regression            | Seq + Struct   | `test`       | `.txt`, `.json`, folder       |
-| `PROTACs`   | Ternary complex prediction in targeted degradation    | Seq + Struct   | `test`       | `.txt`, `.json`, folder       |
+| `PLI_DAVIS` | Protein–ligand binding affinity regression            | Seq + Struct   | `test`       | `.txt`, `.json`, `.sdf`       |
+| `PROTACs`   | Ternary complex prediction in targeted degradation    | Seq + Struct   | `test`       | `.txt`, `.json`, '.sdf'       |
 
 
 ---
@@ -205,17 +205,22 @@ cd protap
 ### 🔹 Protein Function Annotation Prediction (`AFP`)
 
 - **Description**: Predict GO (Gene Ontology) terms for proteins.
-- **Input**: Protein sequence
+- **Input**: Protein sequence and structure
 - **Output**: Multi-label vector representing associated GO terms
 - **Files**:
+  - `AFP/processed_data.json`
+  - `AFP/data_splits.json`
+  - `AFP/nrPDB-GO_annot.tsv`
   - `AFP/nrPDB-GO_test.csv`
 - **Format**:
   - **Input Format**:
-    CSV file with columns:
-    - `sequence_id`: unique ID
-    - `sequence`: amino acid string
-    - [
+    ```AFP/processed_data.json```: json file with key value pair:
+    - `name`: unique ID
+    - `seq`: amino acid sequence
+    - `coords`: protein structure information
+    - `molecular_function`,`biological_process`,`cellular_component`: GO term labels
     ```json
+    - [
       {
         "name": "2P1Z-A",
         "seq": "SKKAELAELVKELAVYVDLRRATLHARASRLIGELLRELTADWDYVA...",
@@ -227,8 +232,23 @@ cd protap
       ...
     ]
     ```
+    ```AFP/data_splits.json```: The division of the train and test datasets
+  - **annotation file Format**:  
+    ```AFP/nrPDB-GO_annot.tsv```：tsv file with multi-column contains the detailed GO term information for all proteins.
+    ```
+    ### PDB-chain	GO-terms (molecular_function)	GO-terms (biological_process)	GO-terms (cellular_component)
+    1A6X-A	        GO:0016874	                    GO:0016053, ... , GO:0032787    GO:1902494
+    ```
+    ```AFP/nrPDB-GO_test.csv```: csv file with multi-column contains the sequence similarity between the test proteins and the training set.
+    ```
+    PDB-chain,<30%,<40%,<50%,<70%,<95%
+    3ONG-B   ,  0 ,  1 ,  1 , 1  , 1
+    1AD3-A   ,  0 ,  0 ,  1 , 1  , 1
+    1FI8-A   ,  0 ,  0 ,  0 , 1  , 1
+    2FWM-X   ,  0 ,  1 ,  1 , 1  , 1
+    ```
   - **Label Format**:
-    One or more GO term IDs (e.g., `GO:0007165`) in a multi-hot encoded label vector
+    One or more GO term IDs (e.g., `GO:0007165`) in a multi-hot encoded label vector, The detailed GO term label information for each protein can be found in the **AFP/nrPDB-GO\_annot.tsv** file.
 - **Metric**: Fmax, AUPR
 
 
@@ -248,5 +268,6 @@ If you use this dataset, please cite:
   }
 ```
 ## Contact
-Please submit GitHub issues or contact Shuo Yan (shuoyan[at]hkust-gz[dot]edu[dot]cn) for any questions related to the source code.
+Please submit GitHub issues or contact Shuo Yan ([syan225@connect.hkust-gz.edu.cn](mailto:syan225@connect.hkust-gz.edu.cn)
+) for any questions related to the source code.