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 3i4e - http://dx.plos.org/10.1371/journal.pone.0086948.g007 Silencing Motifs in the Clr2 Protein from Fission Yeast, Schizosaccharomyces pombe 2014 D Steinhauf, A Rodriguez, D Vlachakis, G Virgo… - PloS one, 2014 - dx.plos.org ... forcefield. The crystal structure of the Haloalkane Dehalogenase (PDB entry: 3QNM) was used for the modeling of C2SM1. Likewise ... the C2SM2. Finally, the Isocitrate Lyase (PDB entry: 3I4E) was used for the modeling of C2SM3. The sequence ...
2 6c87 6byq https://scripts.iucr.org/cgi-bin/paper?rr5159 SIMBAD: a sequence-independent molecular-replacement pipeline 2018 AJ Simpkin, F Simkovic, JMH Thomas- Section D: Structural, 2018 - scripts.iucr.org researchers involved. All cases involve the crystallization of a known contaminant. Examples involving the use of SIMBAD for novel structure solution are available elsewhere, such as PDB entries 6byq, 6c87 and 5wol. Cases illustrating
3 3qxz 3oc7, 4qtp, 3swx, 3qk8, 3qre https://www.sciencedirect.com/science/article/pii/S1476927117300105 Similarity/dissimilarity analysis of protein structures based on Markov random fields 2018 J Wu, T Zhou, J Tao, Y Hai, F Ye, X Liu, Q Dai- Computational biology and, 2018 - Elsevier Recently, the growth of the Protein Data Bank ( PDB ) (Berman et al., 2000) has been accelerated by a large scale As a result, fast and efficient algorithms for protein structure comparison have become more important to take advantage of the huge amount of structural data
4 3gwc - https://pdfs.semanticscholar.org/756c/21ba7ab35e0016d697910450710130b7af99.pdf Similarity in the Amino Acid Sequences of Mycobacterium tuberculosis Protein Targets Involved in Binding Sites of Docking with Thiacetazone 2016 M Mafakheri, S Sardari- Pharm Anal Acta, 2016 - pdfs.semanticscholar.org reviewed and well known M. tuberculosis protein target was chosen (Table 1) then they were downloaded in pdb format from 68 3GWC Transferase -6.24 RRRHHHHM 21. A Structural View of Biology, An Information Portal to 124286 Biological Macromolecular Structures . 22
5 4l82 - https://www.sciencedirect.com/science/article/pii/S2405844019358530 Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) 2019 R Fallahzadeh, B Bambai, K Esfahani, AA Sepahi- Heliyon, 2019 - Elsevier their PDB information, the multiple alignments of these 22 PDB files was done with the DszD. pdb (Fig 1. Predicted three dimensional structure for wild-type DszD enzyme residues (Asn or Ile residue instead of Ala79) were presented on the 3K88 and 4L82 homologous proteins
6 3oks - http://onlinelibrary.wiley.com/doi/10.1111/febs.13293/full Single active‐site mutants are sufficient to enhance serine: pyruvate α‐transaminase activity in an ω‐transaminase 2015 D Deszcz, P Affaticati, N Ladkau, A Gegel… - FEBS …, 2015 - Wiley Online Library ... More distantly related ω-TAms identified in the structure alignments, such as ornithine-AT (PDBcode: 1OAT), 4-aminobutyrate-AT (PDB code: 3OKS and 1SFF), acetylornithine-AT (PDB code:2ORD), l-lysine-epsilon-AT (PDB code: 2CJG), β-phenylalanine-AT (PDB code ...
7 3ecd - http://mcb.asm.org/content/28/14/4507.short Single-stranded oligonucleotides can inhibit cytokine production induced by human toll-like receptor 3 2008 CT Ranjith-Kumar, KE Duffy, JL Jordan? - Molecular and cellular biology, 2008 - Am Soc Microbiol ... (C) The locations of peptides P1 and P2 within the three-dimensional model of 3ECD (PDB accession number, 1ZIW). The peptide spanning residues 211 to 222 is in green, and the one spanning residues 560 to 583 is in yellow. ...
8 3o2e - https://portlandpress.com/bioscirep/article-abstract/doi/10.1042/BSR20202956/226... Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines 2020 T Roret, G Alloing, JM Girardet, T Perrot- Bioscience, 2020 - portlandpress.com protein structures found in the protein databank, we tentatively attributed the changes to the Interestingly, a structure of a BolA_H from the pathogen Coxiella burnetii ligating a Co atom was solved in the frame of a structural genomic initiative for drug design, deposited in ...The coordinates of A. thaliana, B. bovis, and C. burnetii BolA proteins are from previous crystal structures (PDB entries 4PUG, 4PUH, 4PUI, 3O2E and 3TR3)
9 3pfd - https://www.sciencedirect.com/science/article/pii/S0141022918305313 Site-directed mutation to improve the enzymatic activity of 5-carboxy-2-pentenoyl-CoA reductase for enhancing adipic acid biosynthesis 2019 J Yang, Y Lu, Y Zhao, Z Bai, Z Ma, Y Deng- Enzyme and Microbial, 2019 - Elsevier 3PFD was the PDB ID of the template. Therefore, we used 3PFD as the template to build the homology model of Tfu_1647 protein using DS 2017R2 [17] We then used the Deriding-like force field in DS 2017R2 to optimize the structure to ensure that we produced a
10 3v2i - http://www.mdpi.com/2079-6382/5/2/16/htm Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1 2016 PP Ferguson, WB Holloway, WN Setzer, H McFeeters - Antibiotics, 2016 - mdpi.com ... were obtained from the Protein Data Bank and each structure was analyzed for ... The Pth1 setincluded eight bacterial structures: Escherichia coli (PDB 2PTH) [11 ... aeruginosa (4FYJ) [14],Francisella tularensis (3NEA) [15], Burkholderia thailandensis (3V2I) [31], Acinetobacter ...