Update README.md

README.md

@@ -32,3 +32,75 @@ configs:
   - split: test
     path: data/test-*
 ---
+
+# LBA: Ligand Binding Affinity
+
+
+## Overview
+
+In this task, we predict the binding affinity of ligands to their corresponding
+proteins based on the co-crystallized structure of the protein-ligand complex.
+We predict experimentally measured binding affinity as pK, defined as -log(Ki)
+or -log(Kd), depending on which measurement is available.
+
+We derive crystal structures and ligand binding data from PDBBind (Wang et al., 2004),
+a widely-used curated database of protein-ligand complexes with experimental affinities
+derived from literature. We use the 2019 update of the so-called "refined set", a subset
+of complexes selected based on the quality of the structures and the affinity data.
+After filtering ligands which could not be read by RDKit due to invalid bonding data,
+our final dataset consists of 4,463 complexes.
+
+
+## Datasets
+- splits:
+   - split-by-sequence-identity-30: No proteins with seq. id. of more than 30% are in the same set. 
+
+
+## Format
+
+Each entry in the dataset contains the following keys:
+
+    ['input_ids'] The set of atomic numbers for the protein, pocket and ligand atoms concatenated together.
+    ['coords'] The 3D coordinates for the protein, pocket and ligand atoms concatenated together.
+    ['label'] experimentally measured binding affinity as pK.
+    ['token_type_ids'] A mask that corresponds to which inputs_ids/coords belong to the protein, pocket or ligand atoms (0 for protein , 1 for pocket, 2 for ligand)
+
+
+## Citation Information
+
+```
+@article{townshend2020atom3d,
+  title={Atom3d: Tasks on molecules in three dimensions},
+  author={Townshend, Raphael JL and V{\"o}gele, Martin and Suriana, Patricia and Derry, Alexander and Powers, Alexander and Laloudakis, Yianni and Balachandar, Sidhika and Jing, Bowen and Anderson, Brandon and Eismann, Stephan and others},
+  journal={arXiv preprint arXiv:2012.04035},
+  year={2020}
+}
+```
+
+```
+@article{wang2004pdbbind,
+  title={The PDBbind database: Collection of binding affinities for protein- ligand complexes with known three-dimensional structures},
+  author={Wang, Renxiao and Fang, Xueliang and Lu, Yipin and Wang, Shaomeng},
+  journal={Journal of medicinal chemistry},
+  volume={47},
+  number={12},
+  pages={2977--2980},
+  year={2004},
+  publisher={ACS Publications}
+}
+```
+
+```
+@article{liu2015pdb,
+  title={PDB-wide collection of binding data: current status of the PDBbind database},
+  author={Liu, Zhihai and Li, Yan and Han, Li and Li, Jie and Liu, Jie and Zhao, Zhixiong and Nie, Wei and Liu, Yuchen and Wang, Renxiao},
+  journal={Bioinformatics},
+  volume={31},
+  number={3},
+  pages={405--412},
+  year={2015},
+  publisher={Oxford University Press}
+}
+```
+
+