 |
Data parsing - BLUE STAR
STING: Links
|
Introduction:
We would like here to emphasize a very important feature of SMS: Linking
to data from the other BioInformatics sources. We have compiled extensive
list of links so that information (provided by other groups) about a very
same PDB file, can be easily accessed.
Our intention is to continue on providing our own tools and data through
SMS updates, however, we recognize the users need to have most complete
and comprehensive set of information for the given structure; for that
reason, we will continue updating the list of LINKS. Basically, Links
bring complementary information within only one click from the SMS unique
structure descriptors. Make the best use of those LINKS!
It is important to note that all of the links are automatically
bringing the information about very same PDB file being analyzed by SMS. There
are, however, 5 links that require users input in order to get to pertinent
information hidden in the remote data base. We are working to make those links
also completely automatic.
We will show here a few tricks on how to use specific automated
links and get to the other ones, incrementing the volume of information on subject
studied. We will also show here how to use automatic links and data presented
in indicated remote Data bases, in order to get necessary input strings for
the LINKS that require your intervention.
Before all this, let us introduce our own PDB Metrics. It
brings no further information on a given structure, but summary
information on the Protein Data Bank itself.
The Protein Database Metrics or PDB-Metrics is the
new implementation of a discontinued STING module called
PDB_Mining. PDB Metrics provides a summary of the protein structures
deposited in the Protein Data Bank (PDB). It offers a vast
collection of descriptors and means to recover specific PDB
files. PDB-Metrics is a powerful tool for the bioinformatics
researcher to analyze the PDB's collection of protein structure
descriptions from a variety of perspectives, and recover specific
files using a repertoire of alternate criteria.
|
Links to important
external sites, organized in groups by the content of information
offered:
|
See here about useful tricks that you may play in order to get faster to additional
information! On the right side of some
of the LINKs (see table below) we have described what additional
information you may obtain by using that specific site.
Structure Information
| MMDB/NCBI
|
{Use this link also to get abstract
of the original ENTREZ listed publication refered in PDB file} |
| OCA |
{Use this link to see also information
on GeneCards for this particular structure and its gene} |
| IMB_jena |
{Use this link to get directly
to OMIM, Pfam and InterPro data related to given PDB structure. As of now
SMS does NOT offer direct active link to these sites!}
|
| PDB_sum |
|
| NCBI
PDB Codes |
|
| PDB Structures
for EC 3.4.21.1 |
|
| PQS |
|
Structure Classification
| SCOP |
|
| CATH |
|
| FSSP |
|
| CE |
{Use
this site to get structural alignment of any two giv3en structures. Use
Multiple structure SMS Mode to show aligned
strucutres!} |
Contacts
LPC
CSU
Sequence/Structure
Genomics
Presage
GeneCensus
Structural Aligment at
Yale
KEGG
Puma2
Cavity Report
castP
Domains based on Structure
Dali
3Dee
XDomView
NCBI 3D Domains
DDD
Secondary Structure
HSSP
DSSP
Enzyme Information
| SwissProt
|
{Use this
site to get easily to PROSITE annotated sequence mottifs which you can see
on Protein Dossier} |
NiceZyme
Expasy
IUBMB Enzyme Nomenclature
Sequence neighbours
Systers
Super
Family
Pfam
ProtoMap
SMART
InterPro
BRENDA
Protein Mutant Database
Publications - DNA - PROTseq
NCBI
Surface/Structure
| Grass |
{Use this
site to get easily to Grass Surface Pisture Gallery} |
Surface Validation
What
Check
Others
EMP Project
Users Input Required
| PQS |
|
| Metalloprotein |
|
| BLOCKS |
|
| OMIM |
{Use IMB_Jena link to get directly to
OMIM entry related to given PDB structure. As of now SMS does NOT offer
direct active link to these sites!} |
| InterPro
|
{Use IMB_Jena link to get directly to
InterPro entry related to given PDB structure. As of now SMS does NOT offer
direct active link to these sites!} |
| Pfam
|
{Use IMB_Jena link to get directly to
Pfam entry related to given PDB structure. As of now SMS does NOT offer
direct active link to these sites!} |
| Homstrad |
|
