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 6bfu 6nb6, 6nb7, 6nb3, 6tys, 6q04 https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3541361 Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology-and bioinformatic-based predictions 2020 A Grifoni, J Sidney, Y Zhang- -HOST-MICROBE-D, 2020 - papers.ssrn.com with data about immune epitopes, protein structures , and host responses to virus infections (Pickett et al., 2012) glycoprotein structure ( PDB : 6ACD). The calculated surface of the top 10 amino acid residues Non- structural protein 3b 2 0 Protein 7a 2 0 Protein 9b 2 0
2 3hgb - https://www.frontiersin.org/articles/10.3389/fbioe.2020.00965/full?report=reader Mechanism-driven metabolic engineering for bio-based production of free R-lipoic acid in Saccharomyces cerevisiae mitochondria 2020 B Chen, JL Foo, H Ling, MW Chang- Frontiers in bioengineering and, 2020 - frontiersin.org is glycine cleavage system protein H from Mycobacterium tuberculosis ( PDB chain id: 3hgb .1.A domains) were modeled due to the lack of templates with crystal structure of full acetyltransferase component of the pyruvate dehydrogenase complex in Homo sapiens ( PDB
3 5uxx - https://www.nature.com/articles/s41579-020-00450-2 Diverse and unified mechanisms of transcription initiation in bacteria 2020 J Chen, H Boyaci, EA Campbell- Nature Reviews Microbiology, 2020 - nature.com Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. ... Fig 5 Mycobacterium tuberculosis σK–RskA (PDB ID 4NQW; panel Ae) 85, Bartonella quintana σE–NepR (PDB ID 5UXX: panel Af),
4 4k9d - https://www.ingentaconnect.com/contentone/ben/cdth/2020/00000015/00000003/art000... Network-Pharmacology and DFT Based Approach Towards Identification of Leads from Homalomena aromatica for Multi-Target In-Silico Screening on Entamoeba 2020 AK Goswami, HK Sharma, N Gogoi- Current Drug, 2020 - ingentaconnect.com The 3D model of EhGAPDH was predicted based on multiple templates ( PDB IDs: 4O59, 4K9D , 1U8F, 4Z0H, 3V1Y) It uses robust, cross-validated Quantitative Structure Toxicity Relationship (QSTR) models for assessing various measures of toxicity. 3.6
5 3s6l - https://www.frontiersin.org/articles/10.3389/fbioe.2020.613986/pdf Modelled structure of the cell envelope proteinase of Lactococcus lactis 2020 EB Hansen, P Marcatili- Frontiers in bioengineering and, 2020 - frontiersin.org The architecture of the L. lactis CEP shares features with a large number of serine proteases to use current state of the art structure prediction algorithms to establish a structural model of software (version 2.3.3)2 was used for visualization and editing of protein structure PDB files
6 6q04 - https://www.tandfonline.com/doi/abs/10.1080/14760584.2020.1813574 An overview of Middle East respiratory syndrome coronavirus vaccines in preclinical studies 2020 N Zhang, J Shang, C Li, K Zhou, L Du- Expert Review of Vaccines, 2020 - Taylor & Francis Structures of MERS-CoV S1-NTD and MERS-CoV S1-NTD-Neu5Ac complex are presented by ribbon model ( PDB code 6Q04 ) (A) Structure of MERS Both MERS-CoV macro domain and ADP-ribose are presented by ribbon model in green and red, separately ( PDB code 5DUS
7 4dz4 - https://www.frontiersin.org/articles/10.3389/fpls.2020.00987/full?report=reader The neighboring subunit is engaged to stabilize the substrate in the active site of plant arginases 2020 B Sekula- Frontiers in plant science, 2020 - frontiersin.org It is worth noting that the structure of agmatinase from Deinococcus radiodurans ( PDB ID: 1WOG) (Ahn et al., 2004) is ID: 3LHL), agmatinase from Thermoplasma volcanium (TvAGM, PDB ID: 3PZL), and agmatinase from Burkholderia thailandensis (BtAGM, PDB ID: 4DZ4 )
8 6q05 - https://www.biorxiv.org/content/10.1101/2020.04.17.047548v1.abstract Distinct structural flexibility within SARS-CoV-2 spike protein reveals potential therapeutic targets 2020 SH Chen, MT Young, J Gounley, C Stanley, D Bhowmik- BioRxiv, 2020 - biorxiv.org of SARS-CoV-2 ( PDB 6VSB [3]), SARS-CoV-1 ( PDB 6CRZ [15]), MERS- CoV ( PDB 6Q05 [16]), and The trimeric state of the SARS-CoV-2 S protein consists of all three chains in PDB 6VSB Each structure was solvated in the center of a water box with a minimum distance of 15 A
9 3vab - https://www.biorxiv.org/content/10.1101/2020.10.01.322594v1.full-text The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate 2020 VA Bielinski, JK Brunson, A Ghosh, MA Moosburner- bioRxiv, 2020 - biorxiv.org in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA. ... Akin to protomer 2 of PtLYSA, this segment is not included in the structures of DAPDC from Aquifex aeolicus (PDB 2P3E) and Brucella melitensis (PDB 3VAB).
10 3eiy - https://www.biorxiv.org/content/10.1101/2020.07.15.204701v1.abstract Graphein-a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures 2020 AR Jamasb, P Li, T Blundell- bioRxiv, 2020 - biorxiv.org Figure 1. Example outputs from Graphein. A Example protein surface ( 3eiy ). B Example node feature matrix for the residue-level graphs outlined The interaction status data and structure originate from structures of the complexes in the RCSB PDB