Merge branch 'main' into aph-add-radiant

Author: berylrab

datasets/ai3.yaml

@@ -0,0 +1,37 @@
+Name: AI3 Protein-Ligand Binding Affinity Dataset
+Description: >
+  The rapid advancement of computing technologies, particularly artificial intelligence (AI), has revolutionized various domains, including drug discovery. Curated datasets are crucial for developing reliable, generalizable, and accurate models for practical applications. Generating experimental data on a large scale is an expensive and arduous process. In domains such as medical diagnostics where real-life data is hard to obtain, synthetic data has been shown to be extremely valuable. We, teams from IIIT Hyderabad, Intel, AWS, and Insilico Medicine, have performed physics-based calculations (molecular dynamics simulations) on about 20,000 protein-ligand complexes. The dataset comprises molecular dynamics snapshots, binding affinities calculated using the MM-PBSA method, and individual energy components, including electrostatic and van der Waals interactions. DatasetFileFormats essentially incorporate i. 3D coordinates of the protein-ligand complexes (pdb) in tar.gz files, and ii. CSV files containing the energy data. DatasetUsages are on i. ML scoring function for predicting binding affinities of given protein-ligand complexes, ii. Classification models for predicting correct binding poses of ligands, iii. identification of cryptic binding pockets, and iv. optimization of binding features by exploiting the individual components of the energy (experimental data has only the total binding affinity). Further, the novelty of the dataset highlights the fact that existing AI/ML training datasets lack dynamic data and are inherently biased. Further, binding affinity data existing in the literature are obtained from different experimental protocols. Therefore, this dataset has been uniquely created (from the same computational protocols) followed by free energy calculations with molecular dynamics (MD) simulations. The dynamic data-enriched protein-ligand coordinates can be used to effectively train convolutional neural network-based regression models for more accurate binding affinity prediction.
+Documentation: https://github.com/devalab/AI3
+Contact: [email protected]
+ManagedBy: International Institute of Information Technology Hyderabad
+UpdateFrequency: Not updated
+Tags:
+  - pharmaceutical
+  - simulations
+  - health
+  - life sciences
+  - machine learning
+  - protein
+  - molecular dynamics
+  - aws-pds
+License: https://devalab.in/AI3.html
+Resources:
+  - Description: ai3data bucket includes coordinates and the energetics of ~20,000 protein-ligand binding affinity datasets. The subfolders of ai3data bucket consist of Version 1, Version2 and Version 3. Version1 contains the total Size of 10.4 GiB (Initial structure of the protein-ligand complex and the average binding affinities along with average energy components). Version2 contains the total Size of 1.2 TiB (Five trajectories of protein-ligand complex (200 snapshots in all) and the closest two water molecules for each of the protein-ligand complex, and the time series of the binding affinities along with average energy components). Version3 contains the total Size of 10.7 TiB (Five trajectories of completely solvated protein-ligand complex (200 snapshots in all), and the time series of binding affinities along with average energy components).
+    ARN: arn:aws:s3:::ai3data
+    Region: us-east-1
+    Type: S3 Bucket
+DataAtWork:
+  Tutorials:
+    - Title: "AI3: Protein-Ligand Binding Affinity Dataset"
+      URL: https://github.com/devalab/AI3
+      AuthorName: Deva Priyakumar Lab
+      AuthorURL: https://github.com/devalab  
+  Publications:
+    - Title: "PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications"
+      URL: https://www.nature.com/articles/s41597-022-01631-9
+      AuthorName: U. Deva Priyakumar
+      AuthorURL: https://devalab.in/
+    - Title: "PLAS-20k: Extended Dataset of Protein-Ligand Affinities from MD Simulations for Machine Learning Applications"
+      URL: https://www.nature.com/articles/s41597-023-02872-y
+      AuthorName: U. Deva Priyakumar
+      AuthorURL: https://devalab.in

datasets/aodn_animal_acoustic_tracking_delayed_qc.yaml

@@ -28,9 +28,10 @@ Collabs:
     Tags:
       - biodiversity
 Tags:
-- oceans
-- marine mammals
-- biology
+  - aws-pds
+  - oceans
+  - marine mammals
+  - biology
 License: http://creativecommons.org/licenses/by/4.0/
 Resources:
 - Description: Cloud Optimised AODN dataset of IMOS - Animal Tracking Facility - Acoustic
@@ -42,12 +43,12 @@ DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - Animal Tracking Facility - Acoustic Tracking - Quality
       Controlled Detections (2007 - ongoing)
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/animal_acoustic_tracking_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/animal_acoustic_tracking_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/animal_acoustic_tracking_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_animal_ctd_satellite_relay_tagging_delayed_qc.yaml

@@ -44,12 +44,12 @@ DataAtWork:
   Tutorials:
   - Title: Accessing Satellite Relay Tagging Program - Southern Ocean - MEOP Quality
       Controlled CTD Profiles
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/animal_ctd_satellite_relay_tagging_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/animal_ctd_satellite_relay_tagging_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/animal_ctd_satellite_relay_tagging_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_model_sea_level_anomaly_gridded_realtime.yaml

@@ -7,12 +7,12 @@ DataAtWork:
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/model_sea_level_anomaly_gridded_realtime.ipynb
     Title: Accessing IMOS - OceanCurrent - Gridded sea level anomaly - Near real time
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/model_sea_level_anomaly_gridded_realtime.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/model_sea_level_anomaly_gridded_realtime.ipynb
   - AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
 Description: "Gridded (adjusted) sea level anomaly (GSLA), gridded sea level (GSL)\
   \ and surface geostrophic velocity (UCUR,VCUR) for the Australasian region. GSLA\
   \ is mapped using optimal interpolation of detided, de-meaned, inverse-barometer-adjusted\

datasets/aodn_mooring_ctd_delayed_qc.yaml

@@ -31,12 +31,12 @@ Resources:
 DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - Australian National Mooring Network (ANMN) - CTD Profiles
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_ctd_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_ctd_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_ctd_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_mooring_hourly_timeseries_delayed_qc.yaml

@@ -40,12 +40,12 @@ Resources:
 DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - Moorings - Hourly time-series product
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_hourly_timeseries_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_hourly_timeseries_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_hourly_timeseries_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_mooring_satellite_altimetry_calibration_validation.yaml

@@ -58,12 +58,12 @@ Resources:
 DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - SRS Satellite Altimetry Calibration and Validation Sub-Facility
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_satellite_altimetry_calibration_validation.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_satellite_altimetry_calibration_validation.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/mooring_satellite_altimetry_calibration_validation.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_radar_bonneycoast_velocity_hourly_averaged_delayed_qc.yaml

@@ -37,12 +37,12 @@ DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - ACORN - Bonney Coast HF ocean radar site (South Australia,
       Australia) - Delayed mode sea water velocity
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_BonneyCoast_velocity_hourly_averaged_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_BonneyCoast_velocity_hourly_averaged_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_BonneyCoast_velocity_hourly_averaged_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_radar_capricornbunkergroup_velocity_hourly_averaged_delayed_qc.yaml

@@ -49,12 +49,12 @@ DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - ACORN - Capricorn Bunker Group HF ocean radar site (Great
       Barrier Reef, Queensland, Australia) - Delayed mode sea water velocity
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_CapricornBunkerGroup_velocity_hourly_averaged_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_CapricornBunkerGroup_velocity_hourly_averaged_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_CapricornBunkerGroup_velocity_hourly_averaged_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised

datasets/aodn_radar_capricornbunkergroup_wave_delayed_qc.yaml

@@ -48,12 +48,12 @@ DataAtWork:
   Tutorials:
   - Title: Accessing IMOS - ACORN - Capricorn Bunker Group HF ocean radar site (Great
       Barrier Reef, Queensland, Australia) - Delayed mode wave
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_CapricornBunkerGroup_wave_delayed_qc.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_CapricornBunkerGroup_wave_delayed_qc.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/radar_CapricornBunkerGroup_wave_delayed_qc.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised
   - Title: Accessing and search for any AODN dataset
-    URL: https://nbviewer.org/github/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
+    URL: https://github.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     NotebookURL: https://githubtocolab.com/aodn/aodn_cloud_optimised/blob/main/notebooks/GetAodnData.ipynb
     AuthorName: Laurent Besnard
     AuthorURL: https://github.com/aodn/aodn_cloud_optimised