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A framework and predictor based on support vector machine and random walk graph kernel for scoring protein-protein interfaces.
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pdb2sql
Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.
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What pdb2sql can do for you
- a powerful pdb2sql object to convert biomolecular structure data (in PDB format) in SQL database
- strcuture transformation functions (rotations, translations...)
- to calcualte structure interface (contact atoms and residues)
- to calculate structure similarity (iRMSD, lRMSD, FNAT, DockQ...)
pdb2sql easily allows to load a PDB file in an object. Once loaded, the data can be parsed using SQL queries. To facilitate the adoption of the tool simple methods have been developped to wrap the SQL queries in simple methods.
Quick examples and documentation are available on https://pdb2sql.readthedocs.io.
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Journal articles
5- 1.Author(s): Ha Young Kim, Sungsik Kim, Woong-Yang Park, Dongsup KimPublished in Bioinformatics Advances by Oxford University Press (OUP) in 202310.1093/bioadv/vbad011
- 2.Author(s): Daniel T Rademaker, Kevin J van Geemen, Li C XuePublished in Bioinformatics by Oxford University Press (OUP) in 202310.1093/bioinformatics/btad444
- 3.Author(s): Vitalii Stebliankin, Azam Shirali, Prabin Baral, Jimeng Shi, Prem Chapagain, Kalai Mathee, Giri NarasimhanPublished in Nature Machine Intelligence by Springer Science and Business Media LLC in 2023, page: 1042-105310.1038/s42256-023-00715-4
- 4.Author(s): Nicolas Renaud, Yong Jung, Vasant Honavar, Cunliang Geng, Alexandre M.J.J. Bonvin, Li C. XuePublished in SoftwareX by Elsevier BV in 2020, page: 10046210.1016/j.softx.2020.100462
- 5.Author(s): Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C XuePublished in Bioinformatics by Oxford University Press (OUP) in 2019, page: 112-12110.1093/bioinformatics/btz496
Other
3- 1.Author(s): Farzaneh M. Parizi, Yannick J. M. Aarts, Sanna Eerden, Gayatri Ramakrishnan, Li C XuePublished by Cold Spring Harbor Laboratory in 202410.1101/2024.05.27.596020
- 2.Author(s): Vitalii Stebliankin, Azam Shirali, Prabin Baral, Prem Chapagain, Giri NarasimhanPublished by Cold Spring Harbor Laboratory in 202310.1101/2023.01.03.522623
- 3.Author(s): Nicolas Renaud, Cunliang Geng, Sonja Georgievska, Francesco Ambrosetti, Lars Ridder, Dario Marzella, Alexandre M.J.J. Bonvin, Li C XuePublished by Cold Spring Harbor Laboratory in 202110.1101/2021.01.29.425727
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Netherlands eScience Center
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