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 6nb3 - https://www.mdpi.com/1999-4915/13/8/1615 What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2 2021 V Fedorov, E Kholina, S Khruschev, I Kovalenko- Viruses, 2021 - mdpi.com M-protein defines the shape of the viral envelope organizing CoVs assembly in the interaction with all other major structural proteins [9 Computational virology tools contribute greatly to the understanding of viral structure , infectivity and pathogenesis, and design of antiviral drugs ... The models of S-proteins of SARS-CoV and MERS-CoV were based on cryo-EM structures from the Protein Data Bank (PDB) with IDs 6NB3 and 5X58, respectively.
2 3ix6 - https://www.nature.com/articles/s41598-019-48940-5 Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis 2019 B Pandey, S Grover, J Kaur, A Grover- Scientific reports, 2019 - nature.com crystal structures of the ThyA enzyme in Brucella melitensis (PDBID: 3IX6 ), M. tuberculosis 3QJ7) 20 , Enterococcus faecalis ( PDB IF: 6QYA), and Escherichia coli ( PDB ID: 1AXW Comparative analysis of the binding free energy, secondary structure elements, and free energy
3 6ao8 - https://www.sciencedirect.com/science/article/pii/S0022283618302456 Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop 2018 P Stephen, S Ye, M Zhou, J Song, R Zhang- Journal of molecular, 2018 - Elsevier 14]), Campylobacter jejuni (3FNR, unpublished), Plasmodium falciparum (5JLD[15]), Neisseria gonorrhoeae ( 6AO8 , unpublished), Escherichia crystal structure of EcoArgRS in complex with tRNA Arg (deposited under PDB code: 5YYN) representing the first structure of a
4 3meq - https://www.frontiersin.org/articles/10.3389/fmicb.2017.00944 Adaptations to high salt in a halophilic protist: differential expression and gene acquisitions through duplications and gene transfers 2017 T Harding, AJ Roger, AGB Simpson- Frontiers in microbiology, 2017 - frontiersin.org WP_041596283.1), and sequences for characterized NADPH-dependent enzymes from S. cerevisiae (1Q1N), P. perezi (1P0C), Helicobacter pylori (3TWO), Populus tremuloides (1YQD) and Catharanthus roseus (5H81), and for NADH-dependent enzymes from Moraxella sp. (4Z6K), Geobacillus stearothermophilus (3PII), Ralstonia eutropha (3S1L), Brucella suis (3MEQ), and Pseudomonas aeruginosa (1LLU). (B) Maximum-likelihood phylogenetic tree for zinc-dependent alcohol dehydrogenase showing strongly supported clustering (gray
5 6n1f - https://journals.asm.org/doi/abs/10.1128/mbio.00408-23 Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling 2023 P Mutz, W Resch, G Faure, TG Senkevich, EV Koonin- Mbio, 2023 - Am Soc Microbiol Given that all of the models in this work were compared both to the PDB and to the large database of AlphaFold2 ... OPG20 (C10L), OPG31 (C4L), and OPG165 (A37R) are homologs of hydroxylases.... the 2OG-Fe(II) Oxygenase family of Burkholderia pseudomallei (6n1f
6 6ws6 - https://www.frontiersin.org/articles/10.3389/fimmu.2021.652223/full CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro 2021 MT Ma, S Badeti, CH Chen, J Kim- Frontiers in, 2021 - frontiersin.org Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is highly contagious and presents a significant public health issue. Current therapies used to treat coronavirus disease 2019 (COVID-19) include monoclonal antibody cocktail, convalescent plasma, antivirals ... Plasmid construct of S309-CAR. The SFG retroviral vector contains the S309 single chain antibody fragment (accession code 6WS6 on PDB)
7 4whx 3u0g https://www.sciencedirect.com/science/article/pii/S1570963919300494 Functional characterization of PLP fold type IV transaminase with a mixed type of activity from Haliangium ochraceum 2019 YS Zeifman, KM Boyko, AY Nikolaeva- et Biophysica Acta (BBA, 2019 - Elsevier These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further research to understand the structural basis of substrate specificity in these enzymes. Abbreviations PDB entry code, 6H65. 2.8. Structure solution and refinement
8 3pme - http://www.sciencedirect.com/science/article/pii/S096808961000876X The binding of β-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors 2010 KM Alexacou, AC Tenchiu, ED Chrysina… - Bioorganic & medicinal …, 2010 - Elsevier ... 11. The structural results show that all inhibitors are bound with essentially no disturbance ofthe overall protein structure. ... However, upon binding to the catalytic site compounds 3pBr, 3pCl,3pCF3, 3oOH, 3pOMe and 3pMe trigger a significant shift of the 280s loop with ...
9 3v7o - https://link.springer.com/article/10.1007/s00018-019-03303-1 Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription 2019 A Ivanov, P Ramanathan, C Parry, PA Ilinykh- Cellular and Molecular, 2019 - Springer Three-dimensional structural models were built for NP, VP35, VP40, GP, VP30 and VP24 proteins using available crystal structures or by de novo structure prediction to elucidate the potential role of the phosphorylation sites
10 6c49 - https://link.springer.com/article/10.1007/s12010-020-03400-z In silico study of the structure and ligand interactions of alcohol dehydrogenase from cyanobacterium Synechocystis Sp. PCC 6803 as a key enzyme for biofuel 2020 O Haghighi, M Moradi- Applied Biochemistry and Biotechnology, 2020 - Springer with amino acids in Zn ion binding sites along with a slight deviation between Cys 110 in the template and Cys 106 in the homology model in the location of structural Zn PCC 6803 homology model (Cyan) superimposed onto the template crystal structure ( PDB ID: 6C49 ) (Tan