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.
| Structure | Year released | #citations |
|---|---|---|
| 6Q1Y | 2019 | 0 |
| 6TYJ | 2020 | 0 |
| 6UCZ | 2019 | 0 |
| 6UDE | 2019 | 0 |
| 6UDG | 2019 | 0 |
| 6UH2 | 2019 | 0 |
| 6UJD | 2019 | 0 |
| 6ULO | 2019 | 0 |
| 2LHJ | 2011 | 0 |
| 6UWQ | 2020 | 0 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3uve | - | https://www.biorxiv.org/content/10.1101/2021.08.17.456622.abstract | Nicotinate degradation in a microbial eukaryote: a novel, complete pathway extant in Aspergillus nidulans | 2021 | E Bokor, J Amon, M Varga, A Szekeres, Z Hegedus- bioRxiv, 2021 - biorxiv.org | 372 code: 3awd) and carveol dehydrogenase CDH from Mycobacterium avium ( PDB code: 3uve model of HxnN with its closest known 426 structural homolog, FAAH1 ( PDB code: 2vya), |
| 2 | 2lgo | - | https://www.biorxiv.org/content/10.1101/431635v1.abstract | A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures | 2018 | J Zhou, AE Panaitiu, G Grigoryan- bioRxiv, 2018 - biorxiv.org | decompose the target structure to be designed into structural building blocks we call TERMs (tertiary motifs) and use rapid structure search against the Protein Data Bank ( PDB ) to identify sequence patterns associated with each TERM from known protein structures that contain it |
| 3 | 4hwg | - | https://www.biorxiv.org/content/10.1101/535138v1.abstract | Energy Landscape of the Domain Movement in Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase | 2019 | C de Azevedo, AS Nascimento- bioRxiv, 2019 - biorxiv.org | chain without ligands PDB ID Organism Ligands Oligomeric state CV Angle Chain A (deg) Rickettsia bellii ( 4HWG ). We hypothesize that the cubic symmetry observed in this crystal (UDP-GlcNac) and cofactor (UDP) are found bound in the crystal structure (1VGV, 3BEO, 4FKZ |
| 4 | 2n6t | 2n6x, 2n6w, 2n6s | https://www.biorxiv.org/content/10.1101/554931v1.abstract | Conditional Prediction of RNA Secondary Structure Using NMR Chemical Shifts | 2019 | K Zhang, AT Frank- bioRxiv, 2019 - biorxiv.org | chemical shifts were downloaded from the Protein Data Bank ( PDB : http://www. pdb .org) and native NMR-derived structure and the comparison structure is the CS-Folding generated structure 2JYM 2L5Z 2LK3 2MIS 2QH2 1Z2J 1JO7 5UZT 2N3Q 5IEM 2L3E 2N6T 2LPS 2N6S |
| 5 | 3quv | - | https://www.biorxiv.org/content/10.1101/564013v2.abstract | Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification | 2019 | SE Thomas, AJ Whitehouse, K Brown, JM Belardinelli- bioRxiv, 2019 - biorxiv.org | at 1.67 and 1.48 resolution respectively ( PDB codes 6NW6 & 6NW7). The crystals belong 109 region is largely disordered, with residues 162-177 not clearly visible in the apo structure 115 of a deep trefoil knot architecture , made of three distinct untwisted loop regions |
| 6 | 5t8s | - | https://www.biorxiv.org/content/10.1101/622068v2.full.pdf | MCSS-based Predictions of Binding Mode and Selectivity of Nucleotide Ligands | 2020 | R Gonzalez-Aleman, N Chevrollier, M Simoes- bioRxiv, 2020 - biorxiv.org | method based on a coarse-grained model (RNA-LIM) was developed to model the structure of an on the protein-nucleotide complexes currently available in the Protein Data Bank (RCSB PDB (52 less than 2.0 and thus not representative of the currently available structural data |
| 7 | 6b4a | - | https://www.biorxiv.org/content/10.1101/623140v1.abstract | A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers | 2019 | JM Leung, E Nagayasu, YC Hwang, P Pierce, IQ Phan- bioRxiv, 2019 - biorxiv.org | Page 5. 5 more in-depth analysis of the conoid fiber architecture , and a comparison of TgDCX and its eight residues 51-128, rmsd 1.905 ); TgDCX ( 6B4A , chain A, aa150-222) vs DCX domains (Figure 5A, Table 1), we used the structure of TgDCX148-243 as a model for |
| 8 | 3qhx | - | https://www.biorxiv.org/content/10.1101/651067v1.abstract | SolXplain: An Explainable Sequence-Based Protein Solubility Predictor | 2019 | R Mall- bioRxiv, 2019 - biorxiv.org | be used as a scoring function to measure the quality of a tree structure Ht at in [13], devise a fast, greedy and iterative algorithm to identify these optimal tree structures We train our XGBoost classifier on top of physio-chemical (global), sequence and structural features extracted |
| 9 | 3oj6 | 6cuq, 4o3v | https://www.biorxiv.org/content/10.1101/673897v1.abstract | Combining statistical and neural network approaches to derive energy functions for completely flexible protein backbone design | 2019 | B Huang, Y Xu, H Liu- bioRxiv, 2019 - biorxiv.org | To design a backbone, an intended framework is specified first. This framework defines at a very coarse level the intended backbone architecture , including the numbers For each native structure with the given PDB ID, results of four simulations are plotted in different |
| 10 | 4qtp | - | https://www.biorxiv.org/content/10.1101/674879v1.abstract | SiaABCDA threonine phosphorylation pathway that controls biofilm formation in Pseudomonas aeruginosa | 2019 | WH Poh, J Lin, B Colley, N Mller, BC Goh- BioRxiv, 2019 - biorxiv.org | 7NTU Institute of Structural Biology, Nanyang Technological University, Singapore 18 Biofilms are ubiquitous, multicellular structures embedded in a self-made matrix, that can suspended biofilms greatly influence the development, structure and function of their surface-attached |