Update README.md

README.md

@@ -32,3 +32,79 @@ configs:
   - split: test
     path: data/test-*
 ---
+
+# PPI: Protein-Protein Interfaces
+
+
+## Overview
+
+This task relates to predicting which pairs of amino acids, spanning two
+different proteins, will interact upon binding (when they form a complex).
+
+Amino acids are defined as interacting if any of their heavy atoms are within 6
+Angstroms from one another.  
+
+
+## Datasets
+- splits:
+   - DIPS-split: DIPS dataset, split by sequence identity (see add. inf.)
+
+
+## Format
+
+Each entry in the dataset contains the following keys:
+
+
+  ['input_ids'] The set of atomic numbers for both the proteins in the complex concatenated together.
+  ['coords'] The 3D coordinates for both the proteins in the complex concatenated together.
+  ['label'] 1 for interacting, 0 for not interacting.
+  ['token_type_ids'] A mask that corresponds to which inputs_ids/coords belong to the two individual proteins involved in the complex (0 for protein 1 , 1 for protein 2)
+
+
+['atoms_pairs'] (pandas.DataFrame) Atom coordinates of the complexes.
+['atoms_neighbors'] (pandas.DataFrame) Indicates which amino acids interacting in each complex.
+['id'] (str) Contains the PDB filenames, model numbers, and chain IDs of the complexes
+    (format: <PDB_FILE>_<MODEL_NUM1>_<CHAIN_ID1>_<PDB_FILE>_<MODEL_NUM2>_<CHAIN_ID2>)  
+['types'] (dict) Type of each entry.
+['file_path'] (str) Path to the LMDB.
+
+
+## Additional Information
+
+The ensemble consists of a given protein complex, with subunits corresponding 
+to the two individual proteins involved in the complex.
+
+## 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{paszke2019advances,
+  title={Advances in neural information processing systems 32},
+  author={Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and others},
+  journal={Curran Associates, Inc},
+  pages={8024--8035},
+  year={2019}
+}
+```
+
+```
+@article{vreven2015updates,
+  title={Updates to the integrated protein--protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2},
+  author={Vreven, Thom and Moal, Iain H and Vangone, Anna and Pierce, Brian G and Kastritis, Panagiotis L and Torchala, Mieczyslaw and Chaleil, Raphael and Jim{\'e}nez-Garc{\'\i}a, Brian and Bates, Paul A and Fernandez-Recio, Juan and others},
+  journal={Journal of molecular biology},
+  volume={427},
+  number={19},
+  pages={3031--3041},
+  year={2015},
+  publisher={Elsevier}
+}
+```
+