External resources

Links to external resources and databases for structures and models

Data classification:
  • Biology: General information and functionality of the virus as a whole.
  • Structures: Data defining structures determined by experimental methods and referenced via a unique identifier such as a PDB ID.
  • Models: Derived, integrated, or refined structures from multiple data sources prepared for different computational tasks.
  • Therapeutics: Molecules, drugs, antibodies, peptides, etc. which implement targets.
  • Publications: Databases containing pulications, peer-reviewed and pre-prints, relevant to COVID-19

Biology

Coronaviruses 101- Focus on Molecular Virology

Description: In this video, Dr. Glaunsinger talks about the evolution, genetics, and virulence of coronaviruses.

Institution: UC Berkeley and Innovative Genomics Institute

Lab: Glaunsinger lab


Models

Structure Models of All Mature Peptides in 2019-NCoV Genome by C-I-TASSER

Description: This page contains 3D structural models and function annotation for all proteins encoded by the genome of 2019-nCoV, also known as SARS-CoV-2, which is the novel coronavirus causing the COVID-19 pneumonia. The structure models are generated by the C-I-TASSER pipeline, which utilizes deep convolutional neural-network based contact-map predictions to guide the I-TASSER fragment assembly simulations. Benchmark and blind CASP tests showed that C-I-TASSER generates models with a higher accuracy than I-TASSER does, especially for the protein targets lack of homologous templates. For multi-domain targets, the C-I-TASSER structure of individual domains are assembled by DEMO into full length structure.

Institution: University of Michigan

Lab: Yang Zhang


Tristan Croll ISOLDE COVID-19 Models

Description: Models refined by Tristan Croll in ISOLDE

Institution: Cambridge Institute for Medical Research


Solvation Maps for COVID19-Related Protein Targets

Description: This is a free online repository for sharing GIST/HSA data of COVID19 related protein targets. Currently, we have th3 GIST/HSA data for 7 targets (6LU7, 6YB7, 6M03, 6Y84, 6W63, 6JYT and 6W4H).

Institution: Lehman College, City University of New York

Lab: Tom Kurtzman


PubChem

Description: PubChem is a public chemistry database at the National Institutes of Health (NIH). Since the launch in 2004, PubChem has become a key chemical information resource for scientists, students, and the general public. Each month our website and programmatic services provide data to several million users worldwide. PubChem mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. We collect information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others.

Institution: NIH


Structural Biology Task Force GitHub Page

Description: A global public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2.

Organization: Coronavirus Structural Biology Task Force


Therapeutics and Drug Databases

ANI-CAS Antiviral Archive

Description: The dataset files contain low-energy conformers and tautomers for 20,306 from the CAS Antiviral database. Original ~50K molecules were filtered for duplicates and drug-likeness. A collection consists of 67,167 tautomeric structures and ~6.6M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. [DOI: 10.26434/chemrxiv.11819268.v1 ] The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). For each conformer we list total energy, relative energy, and dipole-consistent partial atomic charges. (~5.3GB zip file comprised of SDF files)

Lab: Olexandr Isayev Lab


ANI-FDA Drugs Archive

Description: The dataset files contain low-energy conformers and tautomers of 6,433 FDA approved & investigational drugs. A collection consists of 32,036 tautomeric structures and ~3M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). [DOI: 10.26434/chemrxiv.11819268.v1 ] For each conformer we list total energy, relative energy, and dipole-consistent partial atomic charges. (~2.1GB zip file comprised of SDF files)

Lab: Olexandr Isayev Lab


Drug Repurposing Hub

Description: The Drug Repurposing Hub is a curated and annotated collection of FDA-approved drugs, clinical trial drugs, and pre-clinical tool compounds with a companion information resource. Order library plates to screen yourself or collaborate with the Broad Institute’s Center for the Development of Therapeutics to see if an existing drug may work against your novel target, model system, or indication. While the collection will undoubtedly reveal new uses for developed drugs, its true power is unlocked when applied to discover new biological insights and disease mechanisms.

Institution: University of California, San Francisco

Lab: John Irwin, Brian Shoichet, and others


DrugBank Database

Description: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.

Institution: University of Alberta and The Metabolomics Innovation Centre

Lab: David Wishart


MolPort

Description: MolPort has collected the catalogs of all the major chemical suppliers that cater to drug discovery and created a consolidated database of commercially available screening compounds, building blocks and virtual compounds. These catalogs are up to date and typically synchronized with suppliers inventory daily. MolPort tracks compounds ordered via its platform, and monitors how well suppliers fulfil orders.

Organization: MolPort, Inc.


Open Science Data Portal

Description: NCATS is generating a collection of datasets by screening a panel of SARS-CoV-2-related assays against all approved drugs. These datasets, as well as the assay protocols used to generate them, are being made immediately available to the scientific community on this site as these screens are completed.

Organization: National Center for Advancing Translational Sciences (NCATS)

Institution: National Institutes of Health


Enamine REAL Space

Description: The REAL Space comprises 13 billion make-on-demand molecules and is currently the largest offer of commercially available compounds. The REAL compounds in the Space are assembled via more than 180 well-validated parallel synthesis protocols applied to over 115 000 qualified reagents and building blocks. The synthetic protocols include standard and advanced one-pot procedures. They differ in the number of steps, type of purification, and compound handling, and therefore in the effort required to deliver the products.

Organization: Enamine Ltd


SuperDRUG

Description: SuperDRUG2 database is a unique, one-stop resource for approved/marketed drugs, containing more than 4,600 active pharmaceutical ingredients. We annotated drugs with regulatory details, chemical structures (2D and 3D), dosage, biological targets, physicochemical properties, external identifiers, side-effects and pharmacokinetic data. Different search mechanisms allow navigation through the chemical space of approved drugs. A 2D chemical structure search is provided in addition to a 3D superposition feature that superposes a drug with ligands already known to be found in the experimentally determined protein-ligand complexes.

Institution: University Medicine Berlin

Lab: Structural Bioinformatics Group


SWEETLEAD

Description: The SWEETLEAD database is a cheminformatics database of medicines, drugs, and herbal isolates. It provides a resource for chemical structures and was built by pulling data from several public chemical databases.

Lab: Paul Novick and Vijay Pande


WuXi GalaXi

Description: The first version of this new chemical space approaches 2 billion tangible molecules — 1,686,371,588 (or 1,7*109) to be exact. In close collaboration with WuXi LabNetwork we created a novel chemical space ready for you to download and search. This space contains a lot of unique chemical intellectual property (IP) for your research, and compounds can be created on demand upon request with WuXi. GalaXi has been shaped from WuXi LabNetwork’s building blocks and reaction schemes that have been properly checked to deliver high quality results. High quality processing has been ensured using our CoLibri software.

Organization: BioSolveIT, WuXi LabNetwork


Zinc15 Database

Description: Database of commercially-available compounds for virtual screening. ZINC contains over 230 million purchasable compounds in ready-to-dock, 3D formats. ZINC also contains over 750 million purchasable compounds you can search for analogs in under a minute.

Institution: University of California, San Francisco

Lab: John Irwin, Brian Shoichet, and others


Publications

CORD-19: COVID-19 Open Research Dataset

Description: CORD-19 provides over 52,000 scholarly articles about COVID-19 and the coronavirus family of viruses for use by the research community. This dataset is updated weekly as new research is published in peer-reviewed publications and archives, such as bioRxiv, medRxiv and more.

Organization: Allen Institute for AI


PubChem

Description: PubChem is a public chemistry database at the National Institutes of Health (NIH). Since the launch in 2004, PubChem has become a key chemical information resource for scientists, students, and the general public. Each month our website and programmatic services provide data to several million users worldwide. PubChem mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. We collect information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others.

Institution: NIH