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FireDB - firestar

Structural Biology and Biocomputing Programme. FireDB is a database of Protein Data Bank. Structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt. Accession numbers as well as keywords. Predicts functionally important residues based on the FireDB database. The predictions are based on the local evaluation of alignments between the query sequence and the structures with functional information that are stored in FireDB. firestar. The Server for Quick...

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FireDB - firestar | firedb.bioinfo.cnio.es Reviews

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Structural Biology and Biocomputing Programme. FireDB is a database of Protein Data Bank. Structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt. Accession numbers as well as keywords. Predicts functionally important residues based on the FireDB database. The predictions are based on the local evaluation of alignments between the query sequence and the structures with functional information that are stored in FireDB. firestar. The Server for Quick...

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4 square

5 ligand info

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8 check what's new

9 additional tools

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FireDB - firestar | firedb.bioinfo.cnio.es Reviews

https://firedb.bioinfo.cnio.es

Structural Biology and Biocomputing Programme. FireDB is a database of Protein Data Bank. Structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt. Accession numbers as well as keywords. Predicts functionally important residues based on the FireDB database. The predictions are based on the local evaluation of alignments between the query sequence and the structures with functional information that are stored in FireDB. firestar. The Server for Quick...

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firedb.bioinfo.cnio.es

1

firestar

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Structural Biology and Biocomputing Programme. New per-residue frequency score. Score are available in the results page;. Check the what's new. Page and the Help. Page for more details. Server: predicting functional residues from structural templates and alignment reliability. Upload PDB coordinates file. 1,2] predicts functionally important residues. Predictions are made by evaluating internally generated alignments using SQUARE. Runs HHsearch[3] and PSI-BLAST[4] to generate alignments. The template PDB...

2

FireDB

http://firedb.bioinfo.cnio.es/Php/Help.php

Structural Biology and Biocomputing Programme. FireDB is a fully automated search system for structures in the Protein Data Bank. That contain annotations of residues participating in a functional site. The Database can be accessed by PDB codes or UniProt. The sources of functional residues are protein-ligand atom contacts and the Catalytic Site Atlas. A deteiled description of FireDB output in the FireDB online help. Functional information is highlighted in the alignment. Is available in the firestar.

3

FireDB

http://firedb.bioinfo.cnio.es/Php/ligand/index.html

Structural Biology and Biocomputing Programme. Small ligand information in the PDB. Every chemical compound in the PDB is stored in tables with its description, the PDB structures in which the compound is present and the amino acids pre-calculated to be in contact with the ligand. Ligand searches are allowed using a three letter code as well as keywords that match chemical names or synonyms. All chemical information, including the three letter codes, comes from the mmCIF dictionaries.

4

FireDB

http://firedb.bioinfo.cnio.es/Php/FireDB.php

Structural Biology and Biocomputing Programme. LAST RELEASE: 03 October 2014. FireDB: a database of annotated functionally important residues. FireDB is a database of PDB. Structures and their associated ligands. FireDB also contains the largest set of reliably annotated functionally important residues. A detailed description of the functionalities of this page can be found in the FireDB online help. FireDB is now accesible through RESTful web services. More information also in the FireDB help web page.

5

SQUARE

http://firedb.bioinfo.cnio.es/Php/square.php

Structural Biology and Biocomputing Programme. Server for quick alignment reliability evaluation. Evaluation of Alignment Reliability. The accuracy of sequence-based predictions are sensitive to alignment quality and automatically generated alignments may not be optimal. The per residue alignment scores calculated by SQUARE can give an important insights into the quality of an alignment. Regions defined as reliably aligned by SQUARE are highly likely to be correctly aligned. 1 "Predicting reliable region...

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Structural Biology and Biocomputing Programme. FireDB is a database of Protein Data Bank. Structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt. Accession numbers as well as keywords. Predicts functionally important residues based on the FireDB database. The predictions are based on the local evaluation of alignments between the query sequence and the structures with functional information that are stored in FireDB. firestar. The Server for Quick...

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