What is the dbALP?


    The dbALP is a database of annotated ligands and pockets. Here, we present a publicly available database of 84,600 proteins annotated with putative ligands and pockets. Geometrical pocket search and protein sequence alignment methods were used to extensively find binding ligands and pockets. All collected results are pre-processed and visualized by three dimensional structural view connected with heat-map. The database also provides related information such as ligand residue numbers, ligand's properties, binding pocket positions, its volumes, relevant mutation positions extracted from text-mining literature search, and other external links for protein. dbALP is expected to use drug research efficiently in the way that it predicts binding sites and ligand information of protein only structure. Also, by providing various ligand candidates, this database will help a researcher to select the ligand and interacting pocket in researcher's case.




Workflow






1-1. Protein structure from Protein DataBank (PDB).
1-2. Protein binding pockers are calculated using 'Alpha Pcket Detection software (Pck)'
       [ref. http://schwarz.benjamin.free.fr/Work/Pck/home.htm]
1-3. Aligned protein sequence and ligand information of each residue are gathered using 'HHblits'
       [ref. M Remmert, A Biegert, A Hauser, J Soding, "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment." Nature methods, 2012, 9, 173-175.]
1-4. Literatures are provided for more understanding protein function.
2-1. User can search protein information by PDB, Text, and FASTA format files at Main page.
2-2. PDB and Text results are searched by text-mining.
2-3. Matched FASTA sequences are searched with matched percentages.
2-4. All results are shown by heatmap. Protein pocket position and ligand information are found this result page.




Home



PDB ID search box



- You can search protein structures by PDB ID.
  PDB ID is 4 letters. 4 or less than 4 letters can be searched.



Text search box

 


- You can search protein structures by Text.
  Protein's any information, you know, can be searched. Also, more specifically, you can search protein structure by fields such as structure ID, chain ID, structure title, classification,
  compound, release date, experimental technique(X-ray or NMR etc.), chain length, enzyme No, DB_name, DB_ID, pubmed ID, taxonomy ID, CATH ID, SCOP ID, and Pfam ID.



Protein sequence search box (FASTA)



- You can search protein structures by FASTA sequence. If matched sequences exists in dbALP database, dbALP shows annotated protein structure and ligand information.




Search lists


When you search by PDB ID or Text or FASTA format, the search list is shown with table.



PDB list

PDB list shows lists you search by PDB ID. Lists are consisted of 16 fields. Annotated protein structure can be shown by click PDB ID.






Text list

Text list shows lists you search by Text with fields. Lists are consisted of 16 fields and annotated protein structure can be shown by click PDB ID also.






Sequence list


Sequence list shows lists you search by FASTA format. Lists are consisted of 16 fields and matched rates. Annotated protein structure can be shown by click PDB ID. The dbALP recognize strict FASTA file format. The FASTA file should be consisted of two lines. A sequence in FASTA format begins with a single-line description, followed by line of sequence data. For example, start ">" symbol and the rest of the line is the description. There should be no space between the ">" and the first letter of the identifier. Next protein sequence should be one line. Don't cut the line!




Results


Result page is consisted of 3 sections,

1. Structure information by fields.
2. 3-dimensional protein structure and ligand information with heatmap
3. Literature



1. Structure information by fields


External links are provided.



2. 3-dimensional protein structure and ligand information with heatmap





Results are expressed by Heatmap. Heatmap includes pocket and ligand information. Red color means that pocket volume is bigger than ligand volume, and Blue color means that ligand volume is bigger than pocket volume. White color is no correlation with pocket and ligand. When you click one of the heatmap position, the dbALP shows pocket position and ligand information with 3-dimensional structure. Heatmap is made by DPSP score. Definition of DPSP score is shown below.


Definition of DPSP Score


: pocket index

: predicted ligand index

: # of residues in pocket

: # of matched residues of interacting predicted ligand

: vol possibility sign. ,

: volume of pocket

: volume of ligand (generate by Marvin)

: # of predicted ligand residues()

: # of overlap-ligand residues() in pocket




3. Literature



For more understanding protein function, the dbALP provides literature information.