Add files using upload-large-folder tool

.gitattributes

@@ -57,3 +57,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+extra_experiments/ensembles/Algorithm.pdf filter=lfs diff=lfs merge=lfs -text
+extra_experiments/ensembles/CASP_Specifications_Final.pdf filter=lfs diff=lfs merge=lfs -text
+results/ligands/RESULTS.pose.SUMMARY.csv filter=lfs diff=lfs merge=lfs -text
+results/ligands/RESULTS.pose.SUMMARY.wo_canceled.csv filter=lfs diff=lfs merge=lfs -text

extra_experiments/ensembles/Algorithm.pdf

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extra_experiments/ensembles/CASP_Specifications_Final.pdf

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extra_experiments/ensembles/pdb2quat.py.zip

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extra_experiments/pharma_ligands/L1000.SMILES.tar.gz

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extra_experiments/pharma_ligands/L1000_chymase_README.txt

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+The Chymase dataset, generously provided by F. Hoffmann-La Roche AG (Basel, CH), contains in total 17 protein-ligand(s) complexes after preparation.
+
+Tasks:
+- 17 protein-ligand(s) complexes: BOTH Pose (P) and Affinity (A) prediction.
+
+The stereochemistry is known and is provided for all the ligands, however the protonation might not be optimal and would need to be determined.

extra_experiments/pharma_ligands/L1000_exper_affinity.csv

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+Target ID,STRUCID,ligand_smiles,Compound ID,CHYMASE_IC50_COLI_NH,Task,binding_affinity,rank,binding_affinity_ratio
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extra_experiments/pharma_ligands/L1000_exper_affinity_obsolete.csv

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extra_experiments/pharma_ligands/L1000_exper_struct.tar.gz

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extra_experiments/pharma_ligands/L2000.SMILES.tar.gz

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extra_experiments/pharma_ligands/L2000_cathepsin_README.txt

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+The Cathepsin G dataset, generously provided by F. Hoffmann-La Roche AG (Basel, CH), contains in total 2 protein-ligand(s) complexes.
+
+Tasks:
+- 2 protein-ligand(s) complexes: ONLY Pose (P) prediction.
+
+The stereochemistry is known and is provided for all the ligands, however the protonation might not be optimal and would need to be determined.

extra_experiments/pharma_ligands/L2000_exper_struct.tar.gz

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extra_experiments/pharma_ligands/L3000.SMILES.tar.gz

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extra_experiments/pharma_ligands/L3000_autotaxin_README.txt

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+The Autotaxin dataset, generously provided by F. Hoffmann-La Roche AG (Basel, CH), contains in total 219 protein-ligand(s) complexes after preparation.
+
+Tasks:
+- 93 protein-ligand(s) complexes: BOTH Pose (P) and Affinity (A) prediction;
+- 96 protein-ligand(s) complexes: ONLY Pose (P) prediction;
+- 30 protein-ligand(s) complexes: ONLY Affinity (A) prediction.
+
+The stereochemistry is known and is provided for all the ligands for P and PA tasks but not for A tasks. The protonation state provided might not be optimal and would need to be determined. Some protein-ligand(s) complexes have more than one ligand present in the active site (22 protein-ligand(s) complexes in total). Molecules located nearby (< 4.5 A) the "main" ligand(s) and interacting with specific or non-specific interactions were also included in the SMILES files (.tsv).
+
+The autotaxin protein carries a N-glycosylation on residue Asn497, and was considered as part of the structure (see pdb id 5m7m as example). It contains as well multiple ions: 2 zinc ions are present in the active site. These ions were also considered as part of the autotaxin structure. The position of the carbohydrate and ions won't be taken into account for the final scoring.
+
+Reference:
+@article{hunziker2022synthesis,
+  title={Synthesis, characterization, and in vivo evaluation of a novel potent autotaxin-inhibitor},
+  author={Hunziker, Daniel and Reinehr, Sabrina and Palmhof, Marina and Wagner, Natalie and Biniasch, Thomas and Stute, Gesa and Mattei, Patrizio and Schmitz, Petra and DiGiorgio, Patrick and Hert, J{\'e}r{\^o}me and others},
+  journal={Frontiers in Pharmacology},
+  volume={12},
+  pages={699535},
+  year={2022},
+  publisher={Frontiers Media SA}
+}

extra_experiments/pharma_ligands/L3000_exper_affinity.csv

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+Target ID,Proasis ID,Structure,Compound ID,IC50,Task,binding_affinity,rank,binding_affinity_ratio
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+The Mpro dataset, generously provided by Idorsia Pharmaceuticals Ltd (Allschwil, CH), contains in total 25 protein-ligand(s) complexes. The structure is a homodimer.
+
+Tasks:
+- 25 protein-ligand(s) complexes: ONLY Pose (P) prediction.
+
+The stereochemistry is known and is provided for all the ligands, however the protonation might not be optimal and would need to be determined. Some protein-ligand(s) complexes have more than one ligand present in the active site (20 protein-ligand(s) complexes in total). Molecules located nearby (< 4.5 A) the "main" ligand(s) and interacting with specific or non-specific interactions were also included in the SMILES files (.tsv).
+
+Some ligands are covalently bound to a cysteine residue. Here the attachment points for each covalent inhibitor:
+- L4003, LIG, SMARTS: [cX3][nX2][cX3][nX2] (first atom)
+- L4013, LIG, SMARTS: [C](=[N])[c] (first atom)
+- L4019, LIG, SMARTS: [C](=[N])[c] (first atom)
+- L4023, LIG, SMARTS: [C](=[N])[c] (first atom)
+
+In L4007, Cys145 is chemically modified to S-Hydroperoxycysteine (https://pubchem.ncbi.nlm.nih.gov/compound/S-Hydroperoxycysteine).
+
+Reference:
+@article {Hazemann2024.02.12.579977,
+	author = {Julien Hazemann and Thierry Kimmerlin and Roland Lange and Aengus Mac Sweeney and Geoffroy Bourquin and Daniel Ritz and Paul Czodrowski},
+	title = {Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches},
+	year = {2024},
+	doi = {10.1101/2024.02.12.579977},
+	URL = {https://www.biorxiv.org/content/early/2024/02/13/2024.02.12.579977},
+	eprint = {https://www.biorxiv.org/content/early/2024/02/13/2024.02.12.579977.full.pdf},
+	journal = {bioRxiv}
+}

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+0	LIG	O=C1C[C@@H](C(=O)Nc2cccc(C3CC3)c2)c2cccnc2N1	P
+1	LIG	O=C1C[C@@H](C(=O)Nc2cccc(C3CC3)c2)c2cccnc2N1	P

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