The Windows Azure Protein Databank (PDBA) of 3D Biological Macromolecular Structures

Data

Published by: TeraDiscoveries
Categories: Reference, Health and Wellness, Science & Statistics
Date added: 6/26/2012
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The RCSB Protein Data Bank (http://www.rcsb.org) is the single worldwide repository of information about the 3D structures of large biological molecules. This offering places this information on Windows Azure to be used in bioinformatics. Included is information about the macromolecules’ atomic structure, bond characteristics, residues and crystallography. This offering also contains information on the published work that describes how this data was obtained.

Service root URL

https://api.datamarket.azure.com/TeraDiscoveries/PDB_Access_1/v1/

This service supports both fixed and flexible query. Some queries may include required input parameters. (learn more about query types)

Atom

Input parameters:

Name Sample values Type Required
AtomId Int32
AtomType String
Element String
MMId Int32

Results:

Name Type
AltLoc String
AtomId Int32
AtomType String
ChainId String
Charge String
Element String
ICode String
IsTerm Boolean
MMId Int32
ModelSerialNum Int32
Name String
Occupancy Decimal
ResSeq Int32
Serial Int32
TempFactor Decimal
U11 Int32
U12 Int32
U13 Int32
U22 Int32
U23 Int32
U33 Int32
x Decimal
y Decimal
z Decimal

Author

Input parameters:

Name Sample values Type Required
AuthorId Int32
AuthorName String
MMId Int32

Results:

Name Type
AuthorId Int32
AuthorName String
MMId Int32

CisPep

Input parameters:

Name Sample values Type Required
ChainId1 String
ChainId2 String
CisPepId Int32
ICode1 String
ICode2 String
MMId Int32
ModNum Int32

Results:

Name Type
ChainId1 String
ChainId2 String
CisPepId Int32
ICode1 String
ICode2 String
Measure Decimal
MMId Int32
ModNum Int32
Pep1 String
SeqNum1 Int32
SeqNum2 Int32
SerNum Int32

Cryst1

Input parameters:

Name Sample values Type Required
Cryst1Id Int32
MMId Int32

Results:

Name Type
a Decimal
alpha Decimal
b Decimal
beta Decimal
c Decimal
Cryst1Id Int32
gamma Decimal
MMId Int32
sGroup String
z Int32

Helix

Input parameters:

Name Sample values Type Required
HelixId String
HelxId Int32
MMId Int32
SerNum Int32

Results:

Name Type
Comment String
endChainID String
endICode String
endResName String
endSeqNum Int32
helixClass Int32
HelixId String
HelxId Int32
initChainID String
initICode String
initResName String
initSeqNum Int32
Length Int32
MMId Int32
SerNum Int32

Keyword

Input parameters:

Name Sample values Type Required
KeywordId Int32
MMId Int32

Results:

Name Type
KeywordId Int32
MMId Int32

Link

Input parameters:

Name Sample values Type Required
LinkId Int32
MMId Int32

Results:

Name Type
AltLoc1 String
AltLoc2 String
ChainId1 String
ChainId2 String
ICode1 String
ICode2 String
Length Decimal
LinkId Int32
MMId Int32
Name1 String
Name2 String
ResSeq1 Int32
ResSeq2 Int32
sym1 String
sym2 String

Macromolecule

Input parameters:

Name Sample values Type Required
Classification String
DepositionDate DateTime
IDCode String
MMId Int32
Title String

Results:

Name Type
Caveat String
Classification String
DepositionDate DateTime
DOI String
FileName String
IDCode String
JournalTitle String
MMId Int32
NumberOfModels Int32
ObsoleteDate DateTime
PMID String
Ref String
Refn String
SeqNum Int32
Title String

Matrix

Input parameters:

Name Sample values Type Required
MatrixId Int32
MMId Int32

Results:

Name Type
iGiven String
MatrixId Int32
MMId Int32
Mn1 Decimal
Mn2 Decimal
Mn3 Decimal
n Int32
Serial Int32
Vn Decimal

Origin

Input parameters:

Name Sample values Type Required
MMId Int32
OriginId Int32

Results:

Name Type
MMId Int32
n Int32
On1 Decimal
On2 Decimal
On3 Decimal
OriginId Int32
Tn Decimal

Residue

Input parameters:

Name Sample values Type Required
ResidueId Int32
SeqChainId Int32
SeqNum Int32

Results:

Name Type
ResidueId Int32
SeqChainId Int32
SeqNum Int32

Scale

Input parameters:

Name Sample values Type Required
MMId Int32
ScaleId Int32

Results:

Name Type
MMId Int32
n Int32
ScaleId Int32
Sn1 Decimal
Sn2 Decimal
Sn3 Decimal
Un Decimal

SeqChain

Input parameters:

Name Sample values Type Required
ChainID String
MMId Int32
NumRes Int32
SeqChainId Int32

Results:

Name Type
ChainID String
MMId Int32
NumRes Int32
SeqChainId Int32

Sheet

Input parameters:

Name Sample values Type Required
Id Int32
MMId Int32
SheetID String

Results:

Name Type
curAtom String
curChainID String
curICode String
curResName String
curResSeq Int32
endChainID String
endICode String
endResName String
endSeqNum Int32
Id Int32
initChainID String
initICode String
initResName String
initSeqNum Int32
MMId Int32
prevAtom String
prevChainID String
prevICode String
prevResName String
prevResSeq Int32
sense Int32
SheetID String
Strand Int32

Site

Input parameters:

Name Sample values Type Required
ChainId String
Id Int32
MMId Int32

Results:

Name Type
ChainId String
ICode String
Id Int32
MMId Int32
ResName String
Seq Int32
SeqNum Int32
SiteId String

SSBond

Input parameters:

Name Sample values Type Required
MMId Int32
SSBondId Int32

Results:

Name Type
ChainId1 String
ChainId2 String
ICode1 String
ICode2 String
Length Decimal
MMId Int32
SeqNum1 Int32
SeqNum2 Int32
SerNum Int32
SSBondId Int32
sym1 String
sym2 String

Data contained in the PDB database is free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. Information contained within was sourced from the RSCPDB (http://www.rcsb.org) and their usage terms apply. Link: http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/policies_references.html

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