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A Proposal Tool for Manipulation of a Set of Protein Structures from PDB
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1  Universidade Federal do Rio Grande - FURG


Protein Data Bank (PDB) is a public web database with more than 100,000 biological macromolecular structures. With this large amount of protein structures available on PDB the use of tools for acquisition and analysis of specific sets of biological macromolecules is a necessity. Hence, in this work we propose the development of a tool for acquiring, storing and analyzing specific sets of proteins from the PDB database. The proposed tool runs on desktop environment allowing the user to acquire the structures from the RESTful web-service provided by PDB server. After the acquisition of a set of interesting PDBs the user can manipulate these data in an off-line environment through a local database that stores the information about the characteristics of the structures, for example, ligands, mutations, residues, sequences and docking results. The protein files are locally stored in the users’ computer and can be used, for instance, for molecular docking simulations and alignment of sequences and structures. Having a set of proteins of interest available locally and using our proposed tool the user can perform analysis related to alignments and visualize important proteins characteristics improving the knowledge about specific target. Besides, the user can select PDB files to be visualized on a graphical environment that is integrated in our tool. Other features are related to the exporting of sequence alignments results in csv (comma separated value) format or exporting sequences that have a similar identity in a format that can be easily loaded on graph tools. These alignments allow the user to visualize which proteins are similar and discard those that are not.

Keywords: Protein data bank, sequence alignment, structural alignment.
Comments on this paper
Juan Ruso
Very interesting tool. Where can you get? It is free or paid?
Vinicius Seus
Soon this tool will be able free in the web environment.

Ihosvany Camps
Is it possible to prepare the protein structures with this tools?
Vinicius Seus
The only preparation is in relation to convert the molecule from mol2 format to pdbqt. This conversion add charges to the protein.