Structures

Structural Data for proteins and associated models and simulations

Structures on this page are grouped in tiers:

  1. Viral VS Host
  2. Active interest VS low interest in drug discovery
  3. Therapeutic Modality (Target)
  4. Structure Rating
  5. Model Ratings

Because of the sorting, structures may appear in multiple groups under the first three categories, but they will all link out to the same locations.

Many structural annotations and reviews come from the Coronavirus Structural Task Force.

Data classification:
  • 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.
  • Targets: The biological mechanisms and functions which can be exploited to reduce, prevent, or treat the virus.
  • Proteins: The biological proteins associated with the SARS-CoV-2 virus and host.
  • Simulations: The datasets produced as a result of applying the models to different scientific techniques.

Quick Navigation

3CLpro ACE2 BoAT1 E protein Fc receptor Furin Helicase IL6R M protein Macrodomain N protein NSP1 NSP10 NSP11 NSP14 NSP15 NSP16 NSP2 NSP4 NSP6 NSP7 NSP8 NSP9 ORF10 ORF3a ORF6 ORF7a ORF7b ORF8 PD-1 PLpro RdRP TMPRSS2 fusion core p38 spike virion

Structures of Virion Particle

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Structures of Viral Spike Proteins

Viral Spike Fusion Core

Inhibition of formation of the viral fusion core

Structure of Post Fusion Core of 2019-NCoV S2 Subunit (6LXT)

Additional: Medium-resolution structure of post-fusion core of SARS-CoV-2 S2 subunit

Structure Data and Links: PDBID: 6lxt View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.9 Å

Top Two Models:

Coarse Grained Post Fusion Core of 2019-NCoV S2 Subunit (PDB 6LXT)

Known Target Modalities: Inhibition of Formation of the Viral Fusion Core
Related Proteins: fusion core HR1 HR2
Top Simulations:[See All]

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SARS-CoV-2 Spike (S) glycoprotein

Host immune response

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology (7JX3)

Additional: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with monoclonal antibody S309

Structure Data and Links: PDBID: 7jx3 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.65 Å

Top Two Models:

SARS-CoV-2 Spike Receptor-Binding Domain Bound With S309: ISOLDE Refined Model With N343 Glycan and P337L Mutation

SARS-CoV-2 Spike Receptor-Binding Domain Bound With S309: ISOLDE Refined Model With N343 Glycan and P337A Mutation

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor Host Immune Response
Related Proteins: spike RBD
Top Simulations:[See All]

Folding@home simulations of the SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309

Folding@home simulations of the SARS-CoV-2 spike RBD bound to monoclonal antibody S309


Antibodies to the SARS-CoV-2 Receptor-Binding Domain That Maximize Breadth and Resistance to Viral Escape (7M7W)

Additional: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with monoclonal antibody S2H97

Structure Data and Links: PDBID: 7m7w View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.65 Å

Top Two Models:

SARS-CoV-2 Spike Receptor-Binding Domain Bound With S2H97: ISOLDE Refined Model With N343 Glycan

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor Host Immune Response
Related Proteins: spike RBD
Top Simulations:[See All]

Folding@home simulations of the SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97


Blocking SARS-CoV-2 Spike protein binding to human ACE2 receptor

Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor (2AJF)

Additional: High-resolution cryo-EM structure of the full-length SARS-CoV-1 spike protein bound to human host cell receptor ACE2.

Structure Data and Links: PDBID: 2AJF View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.9 Å

Top Two Models:

Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor in Aqueous Solution

Coarse Grained SPIKE Protein (PDB 2AJF)

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2
Top Simulations:[See All]

Simulations of SARS-CoV and SARS-CoV-2 RBD with ACE2 possessing different patterns of glycosylation

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex in aqueous solution


Crystal Structure of SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2 (6M0J)

Structure Data and Links: PDBID: 6m0j View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.45 Å

Top Two Models:

SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2: ISOLDE Refined Model

SARS-CoV-2 Spike Receptor-Binding Domain: ISOLDE Refined Model Without N343 Glycan

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2
Top Simulations:[See All]

Folding@home simulations of the apo SARS-CoV-2 spike RBD (with glycosylation)

Folding@home simulations of the SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2


Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology (7JX3)

Additional: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with monoclonal antibody S309

Structure Data and Links: PDBID: 7jx3 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.65 Å

Top Two Models:

SARS-CoV-2 Spike Receptor-Binding Domain Bound With S309: ISOLDE Refined Model With N343 Glycan and P337L Mutation

SARS-CoV-2 Spike Receptor-Binding Domain Bound With S309: ISOLDE Refined Model With N343 Glycan and P337A Mutation

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor Host Immune Response
Related Proteins: spike RBD
Top Simulations:[See All]

Folding@home simulations of the SARS-CoV-2 spike RBD bound to monoclonal antibody S309

Folding@home simulations of the SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309


Crystal Structure of Post Fusion Core of 2019-NCoV S2 Subunit (6M1V)

Structure Data and Links: PDBID: 6M1V View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.5 Å

Top Two Models:

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Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike S2
Top Simulations:[See All]

SIRAH-CoV2 initiative - S2 Spike core fragment in postfusion state


Crystal Structure of SARS-CoV-2 Receptor Binding Domain in Complex With Human Antibody CR3022 (6W41)

Additional: Low resolution X-ray structure of human antibody CR3022 bound to the receptor binding domain (RBD) of the spike protein.

Structure Data and Links: PDBID: 6w41 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 3.084 Å

Top Two Models:

Coarse Grained RBD in Complex With Human Antibody CR3022 (PDB 6W41)

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD
Top Simulations:[See All]

SIRAH-CoV2 initiative - S1 Receptor Binding Domain in complex with human antibody CR3022


The 2019-NCoV RBD/ACE2-B0AT1 Complex (6M17)

Additional: High-resolution cryo-EM structure of the full-length SARS-CoV-2 spike protein bound to human host cell receptor ACE2.

Structure Data and Links: PDBID: 6m17 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

Spike Protein in Complex With Human ACE2

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2 BoAT1
Top Simulations:[See All]

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution

Simulations of SARS-CoV and SARS-CoV-2 RBD with ACE2


Structure of the SARS-CoV-2 Spike Glycoprotein (Closed State) (6VXX)

Structure Data and Links: PDBID: 6VXX View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.8 Å

Top Two Models:

Trimeric SARS-CoV-2 Spike Protein (Down State) With and Without Simulation Box in the Absence of Glycan

Trimeric SARS-CoV-2 Spike Glycoprotein (Closed State) in Aqueous Solution

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike
Top Simulations:[See All]

Cluster ensemble of Down asymmetric

Riken CPR TMS, MD2_Down trajectory


Prefusion 2019-NCoV Spike Glycoprotein With a Single Receptor-Binding Domain Up (6VSB)

Structure Data and Links: PDBID: 6VSB View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 3.46 Å

Top Two Models:

Ab 6D3 Bound to SARS-CoV-2 Spike in One RBD Up State

TMPRSS2 Bound to SARS-CoV-2 Spike in One RBD Up State

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD
Top Simulations:[See All]

Riken CPR TMS, TMD1_toUp trajectory

Trajectories of full-length SPIKE protein in the Open state.


Cryo-EM Structure of the SARS-CoV-2 Spike Glycoprotein Bound to Fab 2-4 (6XEY)

Structure Data and Links: PDBID: 6XEY View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 3.25 Å

Top Two Models:

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Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD
Top Simulations:[See All]

SIRAH-CoV2 initiative - RBD triple glycosylated at Asn331, 343, and 481


SARS-CoV-2 Spike Ectodomain Structure (Open State) (6VYB)

Additional: Low-resolution cryo-EM structure of the SARS-CoV-2 ectodomain in the open state.

Structure Data and Links: PDBID: 6vyb View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 3.2 Å

Top Two Models:

Spike Protein in Complex With Human ACE2

Trimeric SARS-CoV-2 Spike Glycoprotein (1Up State) With and Without Simulation Box

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike
Top Simulations:[See All]

Cluster ensemble of 1UP second populated cluster

Cluster ensemble of 1UP/open conformations


Antibodies to the SARS-CoV-2 Receptor-Binding Domain That Maximize Breadth and Resistance to Viral Escape (7M7W)

Additional: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with monoclonal antibody S2H97

Structure Data and Links: PDBID: 7m7w View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.65 Å

Top Two Models:

SARS-CoV-2 Spike Receptor-Binding Domain Bound With S2H97: ISOLDE Refined Model With N343 Glycan

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor Host Immune Response
Related Proteins: spike RBD
Top Simulations:[See All]

Folding@home simulations of the SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97



Structures of Viral Protease, Polymerase, and Nonstructured Proteins

SARS-CoV-2 main protease (3CLpro or NSP5)

3CLpro / Mpro activity

Crystal Structure (Monoclinic Form) of the Complex Resulting From the Reaction Between SARS-CoV-2 (2019-NCoV) Main Protease and Tert-Butyl (1-((S)-1-(((S)-4-(Benzylamino)-3,4-Dioxo-1-((S)-2-Oxopyrrolidin-3-Yl)butan-2-Yl)amino)-3-Cyclopropyl-1-Oxopropan-2-Yl)-2-Oxo-1,2-Dihydropyridin-3-Yl)carbamate (Alpha-Ketoamide 13b) (6Y2F)

Additional: Crystal structure of SARS-CoV-2 main protease provides a basis for drug repurposing studies

Structure Data and Links: PDBID: 6Y2F View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.95 Å

Top Two Models:

Coarse Grained 6y2f (PDB 6Y2F)

Truncated Mpro Based on 6Y2F and Shape-Compliant 3D Conformers

Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: 3CLpro
Top Simulations:[See All]

HADDOCK docking of approved Drugbank set against Mpro with a pharmacophore shape model

HADDOCK docking of approved Drugbank set against Mpro with a geometric shape model


6LZE

Additional: X-Ray crystal structure of SARS-Cov-2 MPro in complex with 11a

Structure Data and Links: PDBID: View 3D
Top Two Models:

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Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: 3CLpro
Top Simulations:[See All]

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Crystal Structure (Orthorhombic Form) of the Complex Resulting From the Reaction Between SARS-CoV-2 (2019-NCoV) Main Protease and Tert-Butyl (1-((S)-1-(((S)-4-(Benzylamino)-3,4-Dioxo-1-((S)-2-Oxopyrrolidin-3-Yl)butan-2-Yl)amino)-3-Cyclopropyl-1-Oxopropan-2-Yl)-2-Oxo-1,2-Dihydropyridin-3-Yl)carbamate (Alpha-Ketoamide 13b) (6Y2G)

Additional: Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors

Structure Data and Links: PDBID: 6Y2G View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.2 Å

Top Two Models:

Coarse Grained 6y2g (PDB 6Y2G)

Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: 3CLpro
Top Simulations:[See All]

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SARS-CoV-2 Main Protease With Unliganded Active Site (2019-NCoV, Coronavirus Disease 2019, COVID-19) (6Y84)

Structure Data and Links: PDBID: 6Y84 View 3D To Be Published

Experimental Method: X-Ray Diffraction | Resolution: 1.39 Å

Top Two Models:

3CLpro Prepared for Simulation in a 120 Cubic a Box for Long Continuous Trajectory

Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: 3CLpro
Top Simulations:[See All]

DESRES 100 µs MD of 3CLpro, All Atom

Folding@home expanded ensemble absolute free energy calculations of potential small molecule inhibitors of the SARS-CoV-2 main protease from the COVID Moonshot


The Crystal Structure of COVID-19 Main Protease in Complex With an Inhibitor N3 (6LU7)

Structure Data and Links: PDBID: 6LU7 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.16 Å

Top Two Models:

SARS-CoV-2 Main Protease (Apo, Monomer) for Folding@home Simulations

Coarse Grained Main Protease Structures (PDB 6LU7 Ligands Removed)

Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: 3CLpro
Top Simulations:[See All]

Riken BDR 10 Microsecond Trajectory System Snapshot every 10ns

AMOEBA 15.14 microsecond trajectory of Main Protease


PanDDA Analysis Group Deposition of Ground-State Model of SARS-CoV-2 Main Protease Screened Against DSI Poised (Enamine), Fraglites and Peplites (Newcastle University), Mini Frags (Astex), York 3D (York University), Electrophile Cysteine Covalent (Weizman Institute) Fragment Libraries (5R8T)

Additional: PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease fragment screening

Structure Data and Links: PDBID: 5R8T View 3D To Be Published

Experimental Method: X-Ray Diffraction | Resolution: 1.27 Å

Top Two Models:

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Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: 3CLpro
Top Simulations:[See All]

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SARS-CoV-2 Macrodomain (NSP3)


SARS-CoV-2 Papain-like protease (NSP3)

3CLpro / Mpro activity

Crystal Structure of ADP Ribose Phosphatase of NSP3 From SARS CoV-2 in the Complex With ADP Ribose (6W02)

Additional: Crystal Structure of ADP ribose phosphatase of PLpro from SARS CoV-2 in the complex with ADP ribose

Structure Data and Links: PDBID: 6W02 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.5 Å

Top Two Models:

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Known Target Modalities: 3CLpro / Mpro Activity
Related Proteins: PLpro
Top Simulations:[See All]

Folding@home simulations of nsp3 macrodomain

SIRAH-CoV2 initiative - Apo ADP-ribose phosphatase of NSP3


Inhibition of PLpro protease activity

The Crystal Structure of Papain-Like Protease of SARS CoV-2 , C111S Mutant (6WRH)

Structure Data and Links: PDBID: 6wrh View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.6 Å

Top Two Models:

SARS-CoV-2 Ligand-Free (PDB 6WRH)

Known Target Modalities: Inhibition of PLpro Protease Activity
Related Proteins: PLpro
Top Simulations:[See All]

Apo SARS-CoV-2 PLPro (from PDB 6WRH C-chain)


X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases (4OW0)

Structure Data and Links: PDBID: 4ow0 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.1 Å

Top Two Models:

SARS-CoV-1 Ligand-Free (PDB 4OW0 Ligand Removed)

SARS-CoV-1 Ligand-Bound (PDB 4OW0)

Known Target Modalities: Inhibition of PLpro Protease Activity
Related Proteins: PLpro
Top Simulations:[See All]

Apo SARS-CoV PLpro

3k bound SARS-CoV PLPro


The Crystal Structure of Papain-Like Protease of SARS CoV-2 (6W9C)

Structure Data and Links: PDBID: 6w9c View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.7 Å

Top Two Models:

SARS-CoV-2 Ligand-Bound (3k Ligand Was Docked to Protein Conformation From 6W9C Ligand-Free MD)

SARS-CoV-2 PLpro: ISOLDE Refined Model

Known Target Modalities: Inhibition of PLpro Protease Activity
Related Proteins: PLpro
Top Simulations:[See All]

3k bound SARS-CoV-2 PLPro (3k docked to frame from trajectory of PDB 6W9C C-chain)

SIRAH-CoV2 initiative - Papain-like Protease


Inhibition of viral polymerases

SARS Coronavirus Papain-Like Protease: Structure of a Viral Deubiquitinating Enzyme (2FE8)

Structure Data and Links: PDBID: 2FE8 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.85 Å

Top Two Models:

Coarse Grained Papain-Like Protease (PDB 2FE8)

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: PLpro
Top Simulations:[See All]

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SARS-CoV-2 RNA Polymerase (NSP12)

Inhibition of viral polymerases

SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors (6M71)

Additional: High-resolution cyro-EM structure of the SARS-CoV-2 NSP7-8 complex with RdRP

Structure Data and Links: PDBID: 6m71 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

Coarse Grained RNA-Dependent RNA Polymerase (PDB 6M71)

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + RTP (Remdesivir Tri-Phosphate) Model for MD Simulations

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8 RdRP
Top Simulations:[See All]

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex, no water or zinc

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution


SARS-CoV-2 RNA-Dependent RNA Polymerase in Complex With Cofactors in Reduced Condition (7BTF)

Structure Data and Links: PDBID: 7BTF View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.95 Å

Top Two Models:

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

SARS-CoV-2 RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: RdRP NSP7 NSP8
Top Simulations:[See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model


Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex (7BV1)

Structure Data and Links: PDBID: 7BV1 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.8 Å

Top Two Models:

SARS-CoV-2 Apo-RdRp Complex (Nsp12+2*nsp8+nsp7) Model for MD Simulations

Coarse Grained Apo NSP7, NSP8 Molecules (PDB 7BV1)

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: RdRP NSP7 NSP8
Top Simulations:[See All]

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model


The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP) (7BV2)

Structure Data and Links: PDBID: 7BV2 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.5 Å

Top Two Models:

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + RTP (Remdesivir Tri-Phosphate) Model for MD Simulations

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8 RdRP
Top Simulations:[See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

HADDOCK docking of approved Drugbank set against RdRp



Helicase coronavirus nonstructural protein 13 (NSP13)

Inhibition of viral polymerases

SARS CoV-2 Spike Protein, Closed Conformation, C3 Symmetry (6ZB5)

Structure Data and Links: PDBID: 6ZB5 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.85 Å

Top Two Models:

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Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: Helicase
Top Simulations:[See All]

MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent. Data were collected for apo, linoleic acid bound and other putative ligands (3x200 ns in each case)


Crystal Structure of the SARS-CoV-2 Helicase at 1.94 Angstrom Resolution (6ZSL)

Structure Data and Links: PDBID: 6ZSL View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.94 Å

Top Two Models:

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Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: Helicase
Top Simulations:[See All]

SIRAH-CoV2 initiative - Helicase



Coronavirus nonstructural protein 1


Coronavirus nonstructural protein 10

Inhibition of viral polymerases

1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2 (6W4H)

Structure Data and Links: PDBID: 6W4H View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.8 Å

Top Two Models:

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Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP16 NSP10
Top Simulations:[See All]

Folding@home simulations of nsp10

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex



Coronavirus nonstructural protein 11


Coronavirus nonstructural protein 14


Coronavirus nonstructural protein 15

Inhibition of viral polymerases

The 1.9 a Crystal Structure of NSP15 Endoribonuclease From SARS CoV-2 in the Complex With a Citrate (6W01)

Structure Data and Links: PDBID: 6W01 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.9 Å

Top Two Models:

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Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP15
Top Simulations:[See All]

SIRAH-CoV2 initiative - NSP15 Endonuclease


The Crystal Structure of COVID-19 Main Protease in Apo Form (6M03)

Structure Data and Links: PDBID: 6M03 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2 Å

Top Two Models:

Coarse Grained COVID-19 Main Protease in Apo Form (PDB 6M03)

Docked Structures of the N-Terminal Natural Substrate to SARS-CoV and SARS-CoV-2 Mpro

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP15
Top Simulations:[See All]

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Coronavirus nonstructural protein 16

Inhibition of viral polymerases

1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex From SARS-CoV-2 (6W4H)

Structure Data and Links: PDBID: 6W4H View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 1.8 Å

Top Two Models:

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Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP16 NSP10
Top Simulations:[See All]

Folding@home simulations of nsp10

SIRAH-CoV2 initiative - NSP16 - NSP10 Complex



Coronavirus nonstructural protein 2


Coronavirus nonstructural protein 4


Coronavirus nonstructural protein 6


Coronavirus nonstructural protein 7

Inhibition of viral polymerases

The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP) (7BV2)

Structure Data and Links: PDBID: 7BV2 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.5 Å

Top Two Models:

Docking-Based Repurposing Study of Approved Drugs Against Truncated RdRp

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8 RdRP
Top Simulations:[See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

HADDOCK docking of approved Drugbank set against RdRp


Crystal Structure of the Co-Factor Complex of NSP7 and the C-Terminal Domain of NSP8 From SARS CoV-2 (6WIQ)

Structure Data and Links: PDBID: 6WIQ View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.85 Å

Top Two Models:

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Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8
Top Simulations:[See All]

SIRAH-CoV2 initiative - Co-factor complex of NSP7 and the C-terminal domain of NSP8


SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors (6M71)

Additional: High-resolution cyro-EM structure of the SARS-CoV-2 NSP7-8 complex with RdRP

Structure Data and Links: PDBID: 6m71 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

SARS-CoV-2 Apo-RdRp Complex (Nsp12+2*nsp8+nsp7) Model for MD Simulations

SARS-CoV-2 Nsp7-Nsp8-Nsp12 RNA Polymerase Complex in Aqueous Solution

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8 RdRP
Top Simulations:[See All]

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model


SARS-CoV-2 RNA-Dependent RNA Polymerase in Complex With Cofactors in Reduced Condition (7BTF)

Structure Data and Links: PDBID: 7BTF View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.95 Å

Top Two Models:

SARS-CoV-2 RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

SARS-CoV-2 Apo-RdRp Complex (Nsp12+2*nsp8+nsp7) Model for MD Simulations

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: RdRP NSP7 NSP8
Top Simulations:[See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model

SIRAH-CoV2 initiative - RNA-dependent RNA polymerase in complex with cofactors NSP7 and NSP8


Crystal Structure of the Nsp7-Nsp8 Complex of SARS-CoV-2 (6YHU)

Structure Data and Links: PDBID: 6YHU View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2 Å

Top Two Models:

---

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8
Top Simulations:[See All]

SIRAH-CoV2 initiative - NSP7-NSP8 complex


Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex (7BV1)

Structure Data and Links: PDBID: 7BV1 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.8 Å

Top Two Models:

SARS-CoV-2 Apo-RdRp Complex (Nsp12+2*nsp8+nsp7) Model for MD Simulations

Coarse Grained Apo NSP7, NSP8 Molecules (PDB 7BV1)

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: RdRP NSP7 NSP8
Top Simulations:[See All]

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model



Coronavirus nonstructural protein 8

Inhibition of viral polymerases

SARS-Cov-2 RNA-Dependent RNA Polymerase in Complex With Cofactors (6M71)

Additional: High-resolution cyro-EM structure of the SARS-CoV-2 NSP7-8 complex with RdRP

Structure Data and Links: PDBID: 6m71 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

SARS-CoV-2 RdRP (NSP12) in Complex With NSP7 and Two Copies of NSP8: ISOLDE Refined Model

Coarse Grained RNA-Dependent RNA Polymerase (PDB 6M71)

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8 RdRP
Top Simulations:[See All]

DESRES-ANTON-10917618 10 µs simulation of SARS-CoV-2 nsp7-nsp8-nsp12 RNA polymerase complex in aqueous solution

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model


SARS-CoV-2 RNA-Dependent RNA Polymerase in Complex With Cofactors in Reduced Condition (7BTF)

Structure Data and Links: PDBID: 7BTF View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.95 Å

Top Two Models:

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

SARS-CoV-2 RdRP (NSP12) in Complex With Cofactors NSP7 and NSP8: ISOLDE Refined Model

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: RdRP NSP7 NSP8
Top Simulations:[See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model


Crystal Structure of the Co-Factor Complex of NSP7 and the C-Terminal Domain of NSP8 From SARS CoV-2 (6WIQ)

Structure Data and Links: PDBID: 6WIQ View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.85 Å

Top Two Models:

---

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8
Top Simulations:[See All]

SIRAH-CoV2 initiative - Co-factor complex of NSP7 and the C-terminal domain of NSP8


Crystal Structure of the Nsp7-Nsp8 Complex of SARS-CoV-2 (6YHU)

Structure Data and Links: PDBID: 6YHU View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2 Å

Top Two Models:

---

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8
Top Simulations:[See All]

SIRAH-CoV2 initiative - NSP7-NSP8 complex


Cryo-EM Structure of the Apo Nsp12-Nsp7-Nsp8 Complex (7BV1)

Structure Data and Links: PDBID: 7BV1 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.8 Å

Top Two Models:

Coarse Grained Apo NSP7, NSP8 Molecules (PDB 7BV1)

SARS-CoV-2 Apo-RdRp Complex (Nsp12+2*nsp8+nsp7) Model for MD Simulations

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: RdRP NSP7 NSP8
Top Simulations:[See All]

Gromacs 300 ns MD of SARS-CoV-2 apo-RdRp model, All Atom model


The Nsp12-Nsp7-Nsp8 Complex Bound to the Template-Primer RNA and Triphosphate Form of Remdesivir(RTP) (7BV2)

Structure Data and Links: PDBID: 7BV2 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.5 Å

Top Two Models:

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + ATP Model for MD Simulations

SARS-CoV-2 RdRp Complex (Nsp12+2*nsp8+nsp7) + RNA Template-Primer + RTP (Remdesivir Tri-Phosphate) Model for MD Simulations

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP7 NSP8 RdRP
Top Simulations:[See All]

Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model

HADDOCK docking of approved Drugbank set against RdRp



Coronavirus nonstructural protein 9

Inhibition of viral polymerases

The Crystal Structure of Nsp9 RNA Binding Protein of SARS CoV-2 (6W4B)

Structure Data and Links: PDBID: 6W4B View 3D To Be Published

Experimental Method: X-Ray Diffraction | Resolution: 2.95 Å

Top Two Models:

---

Known Target Modalities: Inhibition of Viral Polymerases
Related Proteins: NSP9
Top Simulations:[See All]

Folding@home simulations of nsp9

SIRAH-CoV2 initiative - NSP9 RNA binding protein



Structures of Viral Open Reading Frame Proteins

Coronavirus Open Reading Frame 10


Coronavirus Open Reading Frame 3a

Host immune response

Cryo-EM Structure of SARS-CoV-2 ORF3a (6XDC)

Structure Data and Links: PDBID: 6XDC View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

---

Known Target Modalities: Host Immune Response
Related Proteins: ORF3a
Top Simulations:[See All]

SIRAH-CoV2 initiative - Membrane embedded ORF3a



Coronavirus Open Reading Frame 6


Coronavirus Open Reading Frame 7a

Host immune response

STRUCTURE of the SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN (6W37)

Structure Data and Links: PDBID: 6W37 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.9 Å

Top Two Models:

---

Known Target Modalities: Host Immune Response
Related Proteins: ORF7a
Top Simulations:[See All]

SIRAH-CoV2 initiative - ORF7A enconded accessory protein



Coronavirus Open Reading Frame 7b


Coronavirus Open Reading Frame 8


Structures of Viral Membrane Proteins

Membrane Glycoprotein


Structures of Viral Envelope Proteins

Envelope small membrane protein


Structures of Viral Nucleocapsid Proteins

Nucleoprotein

Inhibition of formation of the viral fusion core

Crystal Structure of RNA Binding Domain of Nucleocapsid Phosphoprotein From SARS Coronavirus 2 (6VYO)

Structure Data and Links: PDBID: 6VYO View 3D To Be Published

Experimental Method: X-Ray Diffraction | Resolution: 1.7 Å

Top Two Models:

---

Known Target Modalities: Inhibition of Formation of the Viral Fusion Core
Related Proteins: N protein
Top Simulations:[See All]

SIRAH-CoV2 initiative - RNA binding domain of nucleocapsid phosphoprotein


Crystal Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal RNA Binding Domain (6M3M)

Structure Data and Links: PDBID: 6M3M View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.7 Å

Top Two Models:

---

Known Target Modalities: Inhibition of Formation of the Viral Fusion Core
Related Proteins: N protein
Top Simulations:[See All]

SIRAH-CoV2 initiative - Nucleocapsid protein N-terminal RNA binding domain



Structures of Host Proteins

Angiotensin-converting enzyme 2 (ACE2)

Blocking SARS-CoV-2 Spike protein binding to human ACE2 receptor

The 2019-NCoV RBD/ACE2-B0AT1 Complex (6M17)

Additional: High-resolution cryo-EM structure of the full-length SARS-CoV-2 spike protein bound to human host cell receptor ACE2.

Structure Data and Links: PDBID: 6m17 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

Spike Protein in Complex With Human ACE2

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2 BoAT1
Top Simulations:[See All]

Simulations of SARS-CoV and SARS-CoV-2 RBD with ACE2 possessing different patterns of glycosylation

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution


Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2) (1R42)

Structure Data and Links: PDBID: 1R42 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.2 Å

Top Two Models:

Coarse Grained ACE2 (PDB 1R42 Ligands Removed)

Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2): ISOLDE Refined Model With Glycans

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: ACE2
Top Simulations:[See All]

Folding@home simulations of the SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2

Folding@home simulations of the SARS-CoV-2 spike RBD bound to human ACE2


Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor (2AJF)

Additional: High-resolution cryo-EM structure of the full-length SARS-CoV-1 spike protein bound to human host cell receptor ACE2.

Structure Data and Links: PDBID: 2AJF View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.9 Å

Top Two Models:

Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed With Its Receptor in Aqueous Solution

Coarse Grained SPIKE Protein (PDB 2AJF)

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2
Top Simulations:[See All]

Simulations of SARS-CoV and SARS-CoV-2 RBD with ACE2 possessing different patterns of glycosylation

A 10 µs simulation of a SARS-CoV-1 and SARS-CoV-2 chimera-ACE2 complex in aqueous solution


Crystal Structure of SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2 (6M0J)

Structure Data and Links: PDBID: 6m0j View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.45 Å

Top Two Models:

SARS-CoV-2 Spike Receptor-Binding Domain Bound With ACE2: ISOLDE Refined Model

SARS-CoV-2 Spike Receptor-Binding Domain: ISOLDE Refined Model Without N343 Glycan

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2
Top Simulations:[See All]

Folding@home simulations of the apo SARS-CoV-2 spike RBD (with glycosylation)

Folding@home simulations of the SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2


Inhibitor Bound Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2) (1R4L)

Structure Data and Links: PDBID: 1R4L View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 3 Å

Top Two Models:

Human ACE2 Ectodomain in Aqueous Solution (Inhibitor-Bound Closed State)

Docking-Based Repurposing Study of Approved Drugs Against Truncated Human ACE2 Ectodomain (Inhibitor-Bound Closed State)

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: ACE2
Top Simulations:[See All]

HADDOCK docking of approved Drugbank set against human ACE2 ectodomain

DESRES-ANTON-10875754 10 µs simulation trajectory of the human ACE2 ectodomain in aqueous solution


Structure of SARS-CoV-2 Chimeric Receptor-Binding Domain Complexed With Its Receptor Human ACE2 (6VW1)

Additional: Crystal structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2

Structure Data and Links: PDBID: 6vw1 View 3D Read the Paper

Experimental Method: X-Ray Diffraction | Resolution: 2.68 Å

Top Two Models:

SARS-CoV-2 Trimeric Spike Protein Binding to FDA Approved or Investigational Drug Molecules

Chimeric RBD in Complex With Human ACE2

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: RBD ACE2
Top Simulations:[See All]

DESRES-ANTON-10895671 30 µs of accelerated weighted ensemble MD simulation of a chimeric RBD in complex with ACE2

DESRES-ANTON-10918441 2 µs simulations of 78 FDA approved or investigational drug molecules binding to the ectodomain of human ACE2, no water or ions



Sodium Dependent Neutral Amnio Acid Transporter (BoAT1)

Blocking SARS-CoV-2 Spike protein binding to human ACE2 receptor

The 2019-NCoV RBD/ACE2-B0AT1 Complex (6M17)

Additional: High-resolution cryo-EM structure of the full-length SARS-CoV-2 spike protein bound to human host cell receptor ACE2.

Structure Data and Links: PDBID: 6m17 View 3D Read the Paper

Experimental Method: Electron Microscopy | Resolution: 2.9 Å

Top Two Models:

Coarse Grained RBD/ACE2-B0AT1 Complex (PDB 6M17)

SARS-CoV-2 RBD/ACE2-B0AT1 Complex in Aqueous Solution

Known Target Modalities: Blocking SARS-CoV-2 Spike Protein Binding to Human ACE2 Receptor
Related Proteins: spike RBD ACE2 BoAT1
Top Simulations:[See All]

DESRES-ANTON-10905033 10 µs simulation of the SARS-CoV-2-ACE2 complex in aqueous solution

Trajectory of the Spike protein in complex with human ACE2



Ab Receptor in Host Cells (FcR)


Furin / PACE


Interleukin-6 (IL-6) receptor


Programmed cell death factor 1


p38 Mitogen-Activated Protein Kinase (MPAK)


Transmembrane Protease Serine 2


External Structure Resources

COV3D: A Coronavirus 3D Structure Database

Description: Updated structures of SARS-CoV-2 (COVID-19 virus), SARS-CoV, and MERS-CoV spike proteins, as well as other coronavirus proteins of interest for therapeutics and vaccines.

Institution: Institute for Bioscience and Biotechnology Research, University of Maryland

Lab: Brian Pierce


The Cambridge Structural Database

Description: The Cambridge Structural Database (CSD) is a certified trusted database of fully curated and enhanced organic and metal-organic structures, used by researchers across the globe. Established in 1965, the CSD is the world’s repository for small-molecule organic and metal-organic crystal structures. Containing over one million structures from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists around the world.

Institution: Cambridge Crystallographic Data Centre


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