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.
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3d64 | 3glq, 3n58 | http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00299 | An Inexpensive Method for Selecting Receptor Structures for Virtual Screening | 2015 | Z Huang, CF Wong - Journal of chemical information and , 2015 - ACS Publications | ... SPI also performed better than the best docking energy, the molecular volume of thebound ligand, and the resolution of crystal structure in selecting good receptorstructures for virtual screening. The implications of these findings ... |
| 2 | 3glq | - | http://or.nsfc.gov.cn/bitstream/00001903-5/230830/1/1000014634423.pdf | Inexpensive method for selecting receptor structures for virtual screening | 2015 | Z Huang, CF Wong - Journal of chemical information and modeling, 2015 - or.nsfc.gov.cn | ... 1LI4, 1V8B, 1XWF, 2H5L, 2ZIZ, 2ZJ0, 2ZJ1, 3CE6, 3D64b, 3DHY, 3G1U, 3GLQ, 3H9U, 3N58 ...the results for docking 152 actives and 9942 decoys to 36 crystal structures for BRAF. For thissystem, the SPI identified the best structure (PDB id 3IDP) for virtual screening as the other ... |
| 3 | 3oc6 | - | https://scholarworks.iupui.edu/handle/1805/7949 | Computational protein design: assessment and applications | 2015 | Z Li - 2015 - scholarworks.iupui.edu | ... 53 xiii Page 14. Figure 3.8 Superposition of the target structures ( PDB ID 3PTE and 1B1U, cyan) ... These interactions are utilized in protein structure prediction and protein design. ... structural topology and function through evolution. Experimental techniques, such as ... |
| 4 | 3ek1 | - | http://inderscience.metapress.com/index/F88667Q47093367J.pdf | Conservation of water molecules in protein binding interfaces | 2012 | Z Li, Y He, L Cao, L Wong, J Li - International Journal of Bioinformatics Research and Applications, 2012 - Inderscience | ... Figure 6 Water-contacting structure of four aligned alanine residues in: a rat formyltetrahydrofolate dehydrogenase subunit interface (a, [PDB:2O2P]), and three betaine aldehyde dehydrogenase subunit interfaces (b[PDB:2WOX], c[PDB:1WNB] and d[PDB:3EK1]). ... |
| 5 | 3gvg | 3kxq | http://scholar.google.com/https://bmcbioinformatics.biomedcentral.com/articles/1... | Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding | 2013 | Z Li, Y He, Q Liu, L Zhao, L Wong - BMC , 2013 - bmcbioinformatics.biomedcentral. | ... Domain. PDB. Organism. Resolution (). #Water. #Atoms. ... 1.162. 0.680. 3GVG. M. tuberculosis.1.55. 41. ... Once the aligned wild type and mutant structures are obtained, the 25 water moleculesin wild type are searched in the mutant structure to determine whether it reappears or not ... |
| 6 | 6q09 | - | https://pubs.acs.org/doi/abs/10.1021/acsomega.0c03338 | Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity | 2020 | Z Ma, ML Caldas Nogueira, DP Marchi-Salvador- ACS, 2020 - ACS Publications | Journal Logo. Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity. Zhongxin Ma Zhongxin Ma. Burnett School of Biomedical |
| 7 | 4f3y | 4eqy, 5bq2, 5uy7 | https://www.sciencedirect.com/science/article/pii/S0882401018312464 | Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651 | 2018 | Z Nazir, SG Afridi, M Shah, S Shams, A Khan- Microbial pathogenesis, 2018 - Elsevier | 2.9. Protein 3D structures prediction. The target proteins structural information is vital for predicting immunogenic domains. The structure information of the target proteins was assessed by BLASTp analysis against Protein Data Bank ( PDB ) [42,43]. 2.10. Antigenicity prediction |
| 8 | 5upg | 6cax | https://www.sciencedirect.com/science/article/pii/S0223523423002921 | Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives | 2023 | Z Niu, P Lei, Y Wang, J Wang, J Yang- European Journal of, 2023 - Elsevier | -diphosphate ( PDB code: 2IER); (C) Crystal structure of the E. coli LpxC/LPC-009 complex ( PDB code: 3P3G); (D) Co-crystal structure of LpxC-3 aeruginosa LpxC ( PDB code: 3UHM). |
| 9 | 3ek2 | - | http://www.mdpi.com/1422-0067/15/2/2672/pdf | Paclitaxel Induces Apoptosis in Breast Cancer Cells through Different Calcium-Regulating Mechanisms Depending on External Calcium Conditions | 2014 | Z Pan, A Avila, L Gollahon - International journal of molecular sciences, 2014 - mdpi.com | ... 3 2i6x ?10.3 Porphyromonas gingivalis hydrolase 4 3ek2 ?10.3 Burkholderia pseudomallei eonyl reductase ... Two libraries, ?pdb_subset.py? and ?pdb_centermass.py? from the pdb-tools project (https://code.google.com/p/pdb-tools/) were modified and used in Artemis. ... |
| 10 | 4weo | - | https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.12834 | Rational design of Meso2,3butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations | 2017 | Z Pu, F Ji, J Wang, Y Zhang, W Sun, Y Bao- FEBS letters, 2017 - Wiley Online Library | (A) Structure superposition of the BDHs in Protein Data Bank ( PDB code 1GEG: cyan; 3A28: green; 3WYE: yellow; 4WEO : red). (B) Sequence alignment between the four BDHs. It was prepared with the program Espript 3.0 (http://espript.ibcp.fr) |