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 6vxx - RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental 2021 SK Burley, C Bhikadiya, C Bi, S Bittrich- Nucleic acids, 2021 - Biology; Nucleic Acid Enzymes; RNA and RNA-protein complexes; Structural Biology; Synthetic Biology and Bioengineering; Methods Online; Surveys and Summaries; Database; Web Server. Advance articles; Submit: Author Guidelines;
2 6q06 - Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection 2020 J Fantini, C Di Scala, H Chahinian, N Yahi- International journal of, 2020 - Elsevier N-acetylneuraminic acid (Neu5Ac) was generated with the Hyperchem database. 9-O-acetyl-N-acetylneuraminic acid (9-O-SIA) was retrieved from pdb file 6Q06 [18] Its three-dimensioanl structure was retrieved from pdb file # 4V2O [19]
3 6nb4 6nb7 Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19) 2020 B Shanmugaraj, K Siriwattananon- Asian Pac J Allergy, 2020 - PDB ID 6CS2)72 and the following antibodies are shown in magenta: 80R ( PDB ID 2GHW)73, F26G1 ( PDB ID 3BGF)74, m396 ( PDB ID 2DD8)75, and S230 ( PDB ID 6NB7 (P D B ID 6NB4 ) Structure of SARS coronavirus spike receptor- binding domain complexed with receptor
4 6bfu - Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis 2018 RN Kirchdoerfer, N Wang, J Pallesen, D Wrapp- Scientific reports, 2018 - Structural description of SARS-CoV S 2P ectodomain Structure of the SARS-CoV S 2P ectotodomain fusion peptide 24 adopts a conformation distinct from equivalent regions in (b) alpha- (HuCoV-NL63, 5SZS. pdb 20 ) and (c) deltacoronavirus spikes (PDCV S, 6BFU . pdb 21 ) as
5 6q05 - Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop 2020 JA Jaimes, NM Andr, JS Chappie, JK Millet- Journal of molecular, 2020 - Elsevier Volume 432, Issue 10, 1 May 2020, Pages 3309-3325. Journal home page for Journal of Molecular Biology. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop
6 7jxc 7jxe, 7jxd Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity 2021 EC Thomson, LE Rosen, JG Shepherd, R Spreafico- Cell, 2021 - Elsevier / pdb /surface_glycoprotein/SARS-CoV-2/6m0j/isolde/notes.txt. The 1r42 refined structure differs from the PDB -deposited structure (copied from the 6m17 PDB structure ). ... Key resources table S2H13, S2H14, S2A4, S2X35 IgG Piccoli et al., 2020 PDB: 7JV2, 7JXC, 7JXD, 7JXE
7 6q04 - Controlling the SARS-CoV-2 spike glycoprotein conformation 2020 R Henderson, RJ Edwards, K Mansouri- Nature structural &, 2020 - d, The SARS-2 (left, PDB 6VXX) and MERS (right, PDB 6Q04 ) structures , each with a single protomer depicted in cartoon of the gj angles and dihedrals overlaid on an alignment between a SARS-2 down (cartoon structure with black centroids and lines; PDB 6VXX) and
8 7jx3 7k3q, 7r7n SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape 2021 TN Starr, N Czudnochowski, Z Liu, F Zatta, YJ Park- Nature, 2021 - An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape13, have activity against diverse sarbecoviruses47, and be highly protective through viral neutralization... Structures used were those described in this paper, or previously published structures: ACE2-bound RBD (6M0J)60, CR3022-bound RBD (6W41)61, REGN10987- and REGN10933-bound RBD (6XDG)62, CB6- (LY-CoV016) bound RBD (7C01)63, and S304, S309 and S2H14-bound RBD (7JX3)15.
9 7jv2 7k43, 7jva, 7km8 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants 2021 M Yuan, D Huang, CCD Lee, NC Wu, AM Jackson- Science, 2021 - We therefore investigated the structural and functional 4 ( PDB 6XEY) (27) are shown in pink and light pink, respectively; S2M11 ( PDB 7K43) (30) in orange and yellow; C121 ( PDB 7K8X
10 4q1t - CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum 2017 Y Jiang, F Qian, J Yang, Y Liu, F Dong, C Xu- Nature, 2017 - ... 5b). Assuming that D154 and N155 of cgProB are part of the active site, 3D protein structure modelling indicated that five amino-acid residues (G149, G153, D154, N155, and D156) participate in a complex hydrogen-bonding network with L-proline (Fig. 5b). ... The three-dimensional structural model of cgProB was generated through homology modelling using the SWISS-MODEL server40,41,42 ( The available structure of btProB (PDB code: 4q1t, which shares 38% sequence similar