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SiMPLOD v. 0.6.2 alpha

a Structurally-integrated database for Mutations of PLOD genes

About SiMPLOD

The idea of SiMPLOD emerged during analysis of disease-related mutations on LH/PLOD enzymes after determination of the LH3/PLOD3 crystal structure (Scietti et al., Nature Communications, 2018). SiMPLOD was created by Matteo Campioni , Luigi Scietti and Federico Forneris in the Armenise-Harvard Laboratory of Structural Biology at the University of Pavia. M. Campioni powered the SiMPLOD viewer with the NGL viewer engine and computed the homology models of LH1/ PLOD1 and LH2/PLOD2 starting from LH3/PLOD3 crystal structures using MODELLER; L. Scietti analyzed the LH/PLOD literature, and populated the SiMPLOD database; F. Forneris designed the SiMPLOD website using HTML/CSS/PHP, created the database engine with MySQL and the scripts for administration and update. L. Scietti and F. Forneris are in charge of updates and curation of the SiMPLOD database. Changelog


Is SiMPLOD up-to-date?

Of course! We keep monitoring the literature and we constantly update SiMPLOD with new records. Furthermore, every week, a script automatically compares the records in SiMPLOD with the NCBI ClinVar database (SNP auto-update will follow soon) for updates or new annotations, which are then evaluated manually and uploaded in SiMPLOD with additional annotations if necessary. Last curated update: 2021-09-24 11:38:14.


Can I submit updates/corrections?

Users can submit updates and/or corrections using the contact page. User-submitted changes undergo manual curation prior to SiMPLOD upload (expect a delay of few days).


Citing SiMPLOD

If you find SiMPLOD useful for your research, please cite the paper describing our tool:
L. Scietti, M. Campioni, F. Forneris (2019) SiMPLOD, a structure-integrated database of collagen lysyl hydroxylase (LH/PLOD) enzyme variants. J Bone Min Res, 34(7), 1376-1382. DOI: 10.1002/jbmr.3692. Download EndNote Citation


Acknowledgements

We would like to thank Valentina Speranzini for the constructive feedback, Antonella Chiapparino and Francesca De Giorgi for extensive testing and discussions during creation of the SiMPLOD database.


Financial Support

Creation and maintenance of SiMPLOD are supported by the Giovanni Armenise- Harvard Foundation, the Italian Association for Cancer Research (AIRC), and by the Italian Ministry of Education, University and Research (MIUR): Dipartimenti di Eccellenza Program ( 2018-2022) - Dept. of Biology and Biotechnology "L. Spallanzani", University of Pavia.

Thank you for using SiMPLOD - Created by Fornerislab@UniPV  - Last curated update: 2021-09-24 11:38:14
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