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DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

View Article: PubMed Central - PubMed

ABSTRACT

Background: Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding regions of human and other genomes, considering that a significant portion of eukaryotic genomes code for intrinsically disordered regions in proteins.

Results: DisBind (available at http://biophy.dzu.edu.cn/DisBind) is a collection of experimentally supported binding sites in intrinsically disordered proteins and proteins with both structured and disordered regions. There are a total of 226 IDPs with functional site annotations. These IDPs contain 465 structured regions (ORs) and 428 IDRs according to annotation by DisProt. The database contains a total of 4232 binding residues (from UniProt and PDB structures) in which 2836 residues are in ORs and 1396 in IDRs. These binding sites are classified according to their interacting partners including proteins, RNA, DNA, metal ions and others with 2984, 258, 383, 350, and 262 annotated binding sites, respectively. Each entry contains site-specific annotations (structured regions, intrinsically disordered regions, and functional binding regions) that are experimentally supported according to PDB structures or annotations from UniProt.

Conclusion: The searchable DisBind provides a reliable data resource for functional classification of intrinsically disordered proteins at the residue level.

No MeSH data available.


The front page of DisBind database
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Fig1: The front page of DisBind database

Mentions: Figure 1 shows the top page of DisBind which consists of seven parts: ‘Home’, ‘Classification’ , ‘Browse’, ‘Search’, ‘Blast’,‘Download’ and ‘Help’. Under the ‘Classification’ option, the collected items can be retrieved according to their partners (i.e., DNA, RNA, protein, cofactor/heme, metal ions, substrate/ligand, ATP/GTP and others). All items collected in DisBind numbered from N00001 to N00226 can be also retrieved by clicking ‘Browse’ option. Alternatively, a user can obtain the collected information by inputting any keywords by the ‘Search’ option or protein sequences by the ‘Blast’ option. In addition, all of binding sites along with their secondary structures can be downloaded in the fasta format. ‘Help” page contains detailed explanation of each page and meaning of color codes.Fig. 1


DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins
The front page of DisBind database
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5382478&req=5

Fig1: The front page of DisBind database
Mentions: Figure 1 shows the top page of DisBind which consists of seven parts: ‘Home’, ‘Classification’ , ‘Browse’, ‘Search’, ‘Blast’,‘Download’ and ‘Help’. Under the ‘Classification’ option, the collected items can be retrieved according to their partners (i.e., DNA, RNA, protein, cofactor/heme, metal ions, substrate/ligand, ATP/GTP and others). All items collected in DisBind numbered from N00001 to N00226 can be also retrieved by clicking ‘Browse’ option. Alternatively, a user can obtain the collected information by inputting any keywords by the ‘Search’ option or protein sequences by the ‘Blast’ option. In addition, all of binding sites along with their secondary structures can be downloaded in the fasta format. ‘Help” page contains detailed explanation of each page and meaning of color codes.Fig. 1

View Article: PubMed Central - PubMed

ABSTRACT

Background: Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding regions of human and other genomes, considering that a significant portion of eukaryotic genomes code for intrinsically disordered regions in proteins.

Results: DisBind (available at http://biophy.dzu.edu.cn/DisBind) is a collection of experimentally supported binding sites in intrinsically disordered proteins and proteins with both structured and disordered regions. There are a total of 226 IDPs with functional site annotations. These IDPs contain 465 structured regions (ORs) and 428 IDRs according to annotation by DisProt. The database contains a total of 4232 binding residues (from UniProt and PDB structures) in which 2836 residues are in ORs and 1396 in IDRs. These binding sites are classified according to their interacting partners including proteins, RNA, DNA, metal ions and others with 2984, 258, 383, 350, and 262 annotated binding sites, respectively. Each entry contains site-specific annotations (structured regions, intrinsically disordered regions, and functional binding regions) that are experimentally supported according to PDB structures or annotations from UniProt.

Conclusion: The searchable DisBind provides a reliable data resource for functional classification of intrinsically disordered proteins at the residue level.

No MeSH data available.