DeepRank
Scoring 3D protein-protein interaction models using deep learning
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.
Tags
Programming Language
- Python
- SQL
License
- Apache-2.0
Source code
Participating organizations
Mentions
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iScore: A novel graph kernel-based function for scoring protein-protein docking modelsJune 14, 2019
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iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machinesJanuary 01, 2020
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The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL QueriesMay 28, 2020
Projects with pdb2sql
Contributors
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Cunliang GengNetherlands eScience Center
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Nicolas RenaudNetherlands eScience Center
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