Foldingathome COVID-19 Datasets

Tutorials

• Folding@home COVID-19 efforts by Folding@home Consortium
  

Tools & Applications

• SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2 (953.7 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 COVID Moonshot absolute free energy calculations by The Voelz lab at Temple University
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) dimer simulations: A 2.9 ms dataset of the SARS-CoV-2 main viral protease (apo, dimer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 2.6 ms equilibrium dataset of the SARS-CoV-2 main viral protease (apo, monomer) by The Chodera lab at MSKCC
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 6.4 ms dataset of the SARS-CoV-2 main viral protease (apo, monomer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp10 dataset: A 6.1 ms dataset of the SARS-CoV-2 nsp10 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp3 macrodomain dataset: An 11 ms dataset of the SARS-CoV-2 nsp3 macrodomain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp3 pl2pro domain dataset: An 731 µs dataset of the SARS-CoV-2 nsp3 pl2pro domain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp7 simulations: A 3.7 ms dataset of the SARS-CoV-2 nsp7 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp8 simulations: A 1.8 ms dataset of the SARS-CoV-2 nsp8 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp9 simulations: A 9 ms dataset of the SARS-CoV-2 nsp9 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 RNA polymerase (nsp12, RdRP) dataset: A 3.4 ms dataset of the SARS-CoV-2 nsp12 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 spike protein dataset: A 1.2 ms dataset of the SARS-CoV-2 spike protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 spike RBD (with glycosylation) (1.8 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD (without glycosylation) (1.9 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to human ACE2 receptor (173.8 us): Wild-type and mutant simulations by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97 (623.7 us) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S309 (1.1 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309 (907.0 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309 (923.2 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  

Publications

• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity by Emma C. Thomson, Laura E, Rosen, James G. Shepherd, et al.
  
• SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape by Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu, et al.
  
• SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome by Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, View ORCID ProfileRafal P. Wiewiora, Matthew F. D. Hurley, Aoife M Harbison, Carl A Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman
  

Open Targets

Tutorials

• Autoimmune colocalisations by Open Targets Team
  
  
• Autoimmune credible sets by Open Targets Team
  
  
• ChEMBL Evidence Data Download by Open Targets Team
  
  
• Exploration of Open Targets datasets by Open Targets Team
  
  
• Getting started with the Open Targets Platform GraphQL API by Helena Cornu
  
• Open Targets informatics tools by Helena Cornu
  
• Platform datasets on AWS by Daniel Suveges
  
  

Tools & Applications

• Open Targets Platform API by Open Targets
  
• Open Targets Platform MCP by Open Targets
  
• Open Targets Platform Web Application by Open Targets
  

Publications

• Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery by Annalisa Buniello
  

Alliance of Genome Resources

Tutorials

• Alliance of Genome Resources AWS Data Access Tutorials by Alliance of Genome Resources Consortium
  

Tools & Applications

• Alliance of Genome Resources Portal by Alliance of Genome Resources Consortium
  
• FlyBase - Drosophila Database by FlyBase Consortium
  
• MGI - Mouse Genome Database by MGI
  
• RGD - Rat Genome Database by RGD
  
• SGD - Saccharomyces Genome Database by SGD
  
• WormBase - C. elegans Database by WormBase Consortium
  
• Xenbase - Xenopus Database by Xenbase
  
• ZFIN - Zebrafish Database by ZFIN
  

Publications

• Alliance of Genome Resources Portal - unified model organism research platform by Alliance of Genome Resources Consortium
  

Steinegger Lab Datasets

Tutorials

• ColabFold Tutorial by Ovchinnikov S, Mirdita M and Steinegger M
  
• ColabFold User Guide by Mirdita M and Ovchinnikov S
  
• Foldseek User Guide by Mirdita M and Steinegger M
  

Tools & Applications

• ColabFold Google Colab Notebook by Ovchinnikov S, Mirdita M and Steinegger M
  
• Foldseek Search Server by van Kempen M, Kim S, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, et al.
  
• Run ColabFold on your local computer by Moriwaki Y
  

Publications

• ColabFold: Making protein folding accessible to all by Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M
  
• Fast and accurate protein structure search with Foldseek by van Kempen M, Kim S, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, et al.
  
• MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets by Steinegger M and Söding J
  

SnpEff & SnpSift Genomic Variant Annotation Databases

Tutorials

• Building Custom SnpEff Databases by SnpEff Project
  
• SnpEff Documentation by Pablo Cingolani
  
• SnpEff Introduction and Quick Start by SnpEff Project
  

Tools & Applications

• SnpEff by Pablo Cingolani
  
• SnpSift by Pablo Cingolani
  

Publications

• A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 by Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM
  
• Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift by Cingolani P, Patel VM, Coon M, Nguyen T, Land SJ, Ruden DM, Lu X
  

Protein Data Bank 3D Structural Biology Data

Tutorials

• File Download Services by RCSB PDB
  
• Get to Know a Dataset: Protein Data Bank 3D Structural Biology Data by RCSB PDB
  
• PDB 101 by RCSB PDB
  

Publications

• Announcing the worldwide Protein Data Bank by Berman, H., Henrick, K. & Nakamura, H.
  
• Protein Data Bank: the single global archive for 3D macromolecular structure data by wwPDB consortium
  

BUSCO Datasets

Tutorials

• BUSCO - from QC to gene prediction and phylogenomics by Matthew Berkeley
  

Publications

• BUSCO - assessing genomic data quality and beyond. by Mosè Manni, Matthew R. Berkeley, Mathieu Seppey, Evgeny M. Zdobnov
  
• BUSCO Update - Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. by Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov
  
• OrthoDB and BUSCO update - annotation of orthologs with wider sampling of genomes. by Fredrik Tegenfeldt, Dmitry Kuznetsov, Mosè Manni, Matthew Berkeley, Evgeny M Zdobnov, Evgenia V Kriventseva
  

Basic Local Alignment Sequences Tool (BLAST) Databases

Tools & Applications

• BLAST on the Cloud with NCBI’s ElasticBLAST by Sixing Huang
  
• BLAST+ Docker by NCBI BLAST
  

Publications

• BLAST+: Architecture and Applications by Christiam Camacho 1 , George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden
  
• Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs by S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman
  

AI3 Protein-Ligand Binding Affinity Dataset

Tutorials

• AI3: Protein-Ligand Binding Affinity Dataset by Deva Priyakumar Lab
  

Publications

• PLAS-20k: Extended Dataset of Protein-Ligand Affinities from MD Simulations for Machine Learning Applications by U. Deva Priyakumar
  
• PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications by U. Deva Priyakumar
  

CZ Grand Challenges - Imaging MIT Licensed data and models

Tutorials

• Documentation for CELL-Diff by CZI
  
• Documentation for SubCell by CZI
  
• Quickstart Tutorial for CELL-Diff by CZI
  
• Quickstart Tutorial for SubCell by CZI
  

Publications

• CELL-Diff: Unified diffusion modeling for protein sequences and microscopy images by Zheng Dihan, Bo Huang
  
• SubCell: Vision foundation models for microscopy capture single-cell biology by Ankit Gupta, Zoe Wefers, Konstantin Kahnert, Jan N Hansen, William D. Leineweber, Anthony Cesnik, Dan Lu, Ulrika Axelsson, Frederic Ballllosera Navarro, Theofanis Karaletsos, Emma Lundberg
  

CZ Grand Challenges - Transcriptomic MIT Licensed data and models

Tutorials

• Documentation for scGenePT by CZI
  
• Documentation for Transcriptformer by CZI
  
• Quickstart Tutorial for Transcriptformer by CZI
  
• scGenePT Perturbation Prediction Tutorial by CZI
  

Publications

• A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model by Pearce, J. D., et. al.
  
• scGenePT: Is language all you need for modeling single-cell perturbations? by Ana-Maria Istrate, Donghui Li, Theofanis Karaletsos
  

DeepDrug Protein Embeddings Bank (DPEB)

Tutorials

• Aggregating and Clustering AlphaFold2 Embeddings from DPEB by Md. Saiful Islam Sajol
  

Tools & Applications

• DPEB Explorer Tool by DeepDrug Lab
  

Publications

• A Multimodal Human Protein Embeddings Database - DeepDrug Protein Embeddings Bank (DPEB) by Sajol MSI, Rajasekaran M, Bess A, Alvin C, Mukhopadhyay S
  

OpenFold3 Training Data

Tutorials

• Deploying OpenFold3 with NVIDIA NIMs on Brev & AWS EC2 by Glòria Macià
  

Publications

• OpenFold3-preview2 Technical Report by The OpenFold3 Team
  
• OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization by Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J, et al
  

OpenProteinSet

Tutorials

• Run inference at scale for OpenFold, a PyTorch-based protein folding ML model, using Amazon EKS by Shubha Kumbadakone, Ankur Srivastava, and Sachin Kadyan
  Amazon EKSAmazon FSx

Publications

• OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization by Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J, et al
  
• OpenProteinSet: Training data for structural biology at scale by Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Jarosch, Lukas; Berenberg, Daniel; Fisk, Ian, et al
  

ProteinGym

Tutorials

• Scoring ProteinGym assays with TranceptEVE by Daniel Ritter
  

Tools & Applications

• ProteinGym website by Pascal Notin & Daniel Ritter
  

Publications

• ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design by Pascal Notin, et al.
  

E11bio PRISM

Tutorials

• E11.Bio PRISM OpenData by Arlo Sheridan & Johan Winnubst
  

Tools & Applications

• Volara by Arlo Sheridan & Will Patton
  

FLAb: Fitness Landscapes for Antibodies

Tutorials

• FLAb tutorial: Benchmarking a protein language model for antibody expression prediction by Michael Chungyoun
  

Publications

• FLAb: Benchmarking deep learning methods for antibody fitness prediction by Michael Chungyoun and Jeffrey J. Gray
  

UniProt

Tutorials

• Exploring the UniProt protein knowledgebase with AWS Open Data and Amazon Neptune by Eric Greene, Rafa Xu, Yuan Shi (AWS)
  Amazon Neptune
• UniProt SPARQL by Swiss-Prot Group at SIB Swiss Institute of Bioinformatics
  

Conformational Space of Short Peptides

Tutorials

• Intro to Conformational Space of Short Peptides by Sebastian Bassi and Virginia Gonzalez
  

Single-Cell Atlas of Human Blood During Healthy Aging

Publications

• Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB−CD8+ memory T cells and accumulation of type 2 memory T cells by Terekhova M, Swain A, Bohacova P, Aladyeva E, Arthur L, et al
  

ZINC Database

Publications

• ZINC Database by John Irwin
  

BioLiP

Tutorials

• BioLiP API usage by Zhang Lab
  

Publications

• BioLiP2: an updated structure database for biologically relevant ligand-protein interactions by Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang
  
• BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions by Jianyi Yang, Ambrish Roy, and Yang Zhang
  

CZ Grand Challenges - Imaging BSD licensed data and models

Tutorials

• Documentation for Cytoland by CZI
  
• Quickstart Tutorial for Cytoland by CZI
  

Publications

• Cytoland: robust virtual staining of landmark organelles by Liu, Hirata-Miyasaki, et al.
  

SocialGene RefSeq Databases

Tutorials

• How to use SocialGene on AWS by Chase M. Clark
  Amazon EC2

Tools & Applications

• socialgene on pypi.python.org - python module for creating and interacting with SocialGene Neo4j databases by Chase M. Clark
  

Publications

• Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene. by C. M. Clark, J. C. Kwan