SSGCID
Seattle Structural Genomics Center for Infectious Disease

Cited Structures: list of articles citing SSGCID structures

We are actively tracking the number of publications by the scientific community which reference our structures, whether in the main text, figure captions or supplementary material. Selected articles are manually reviewed. Publications by SSGCID authors are excluded from the manually reviewed list. From our manual curation results, we estimate that the false positive rate might be as high as 50% for some structures.

This list was obtained from Google Scholar searches using an API provided by Christian Kreibich.

Cited structures

Manually reviewed citations

# PDB Additional SSGCID structures cited Link Title Year Citation Highlighted abstract
1 7lxy 7ly2, 7lxz, 7ly3 https://www.nature.com/articles/s41423-021-00752-2 Neutralizing antibodies for the prevention and treatment of COVID-19 2021 L Du, Y Yang, X Zhang- Cellular & Molecular Immunology, 2021 - nature.com Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) initiates the infection process by binding to the viral cellular receptor angiotensin-converting enzyme 2 through the receptor-binding domain (RBD) in the S1 subunit of the viral spike (S) protein. ... a–e Cryo-EM structures of the SARS-CoV-2 S trimer bound to NTD-targeting nAbs a S2L28 (PDB 7LXZ), b S2M28 (PDB 7LY2), c S2X333 (PDB 7LXY), d 4-8 (PDB 7LQV), and e 4A8 (PDB 7C2L).
2 7lxz 7ly2 https://www.cell.com/cell-reports/pdf/S2211-1247(21)01401-7.pdf Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain 2021 G Cerutti, Y Guo, P Wang, MS Nair, M Wang, Y Huang- Cell reports, 2021 - cell.com We produced a structural superposition of all NTD-directed antibodies deposited in the PDB , superposed on NTD Ca atoms, in the context of SARS-CoV-2 spike trimer (Figure 2A). ... Figure S1. Sequence alignment for 5-7 with their corresponding germline genes, Related to Figures 1 and 2. 7LXZ McCallum et al., 2021
3 7ly3 7ral https://www.cell.com/cell-reports/pdf/S2211-1247(22)00798-7.pdf Cryo-EM structures of SARS-CoV-2 Omicron BA. 2 spike 2022 V Stalls, J Lindenberger, SMC Gobeil, R Henderson- Cell Reports, 2022 - cell.com The structures used in this analysis included PDB IDs 7KE8 (G6141), 7KE6 (G6142), 7KE7 (G6143), 7KE4 (G6144), 7LWS (Alpha), 7LYL (Beta), 8CSA (TM), 7LWL (Mk1), 7LWI (Mk2),
4 7m53 - https://www.nature.com/articles/s42003-022-03262-7 Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit 2022 NK Hurlburt, LJ Homad, I Sinha, MF Jennewein- Communications, 2022 - nature.com a Structural alignment of stem helix peptides to CV3-25 Fab and B6 Fab (PDBid: 7M53 ) shown The CV3-25/peptide structure has been deposited in the PDB (7RAQ). The negative stain
5 7m53 - https://www.cell.com/immunity/pdf/S1074-7613(23)00079-1.pdf Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease 2023 P Zhou, G Song, H Liu, M Yuan, W He, N Beutler, X Zhu- Immunity, 2023 - cell.com Glycan molecules (sticks, white) were modeled (based on structure in PDB : structures . Key epitope residues are buried in the stem-helix bundle (green) in prefusion spike... Figure S7. Structural comparison of antibodies targeting the coronavirus spike S2 stem helix. ... CV3-25 (7NAB), B6 (7M53), and IgG22 (7S3N). S
6 7n8i - https://www.nature.com/articles/s41592-022-01645-6 Improved AlphaFold modeling with implicit experimental information 2022 TC Terwilliger, BK Poon, PV Afonine, CJ Schlicksup- Nature, 2022 - nature.com To emulate the situation where no similar structure is present in the PDB , templates from the PDB were not used. For each protein we then examined the four AlphaFold models
7 7r7n - https://www.nature.com/articles/s41467-022-28882-9 Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain 2022 G Ye, B Liu, F Li- Nature communications, 2022 - nature.com The atomic models generated in this study have been deposited into the PDB with accession number 7TGW (omicron open spike), 7TGX (prototypic open spike), and 7TGY (prototypic ... Forty-nine PDBs of neutralizing antibody/RBD complexes were analyzed using PDBePISA ... 7r7n, 7sn2. Fab: antigen-binding fragment.
8 7r7n - https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(22)00311-5/fullt... Monoclonal antibody therapies against SARS-CoV-2 2022 D Focosi, S McConnell, A Casadevall- The Lancet Infectious, 2022 - thelancet.com PDB 7K8M). Antibody binding classes 14 are displayed as mesh space-filling. (C) Structures in complex with a single RBD domain ( PDB 6XEY). Antibody binding classes RBS-A, RBS- ... S2D10633 7r7n RBM class III*
9 7so9 - https://dergipark.org.tr/en/pub/biotechstudies/issue/77337/1332403 Omicron variants bind to human angiotensin-converting enzyme 2 (ACE2) much stronger due to higher number of charged-charged interactions 2023 S Kalyoncu- Biotech Studies - dergipark.org.tr Three dimensional RBD domain structures of many variants used in this study were already in RCSB PBD database ( PDB IDs: 7EKF for Alpha, 7EKG for Beta, 7EKC for Delta, 7SO9 for