Description of query pages
Description about modeling and visualization
The modeling step provides the user with the ability to choose which nsSNPs to map, and after completion, a user can instantly visualize the models with the Friend applet.
Choosing nsSNPs to map
If the nsSNPs are available
to choose for modeling, they will appear
as a yellow checkbox. It is possible to choose all available nsSNPs
for the same model.
Visualization of models with Friend applet
Friend applet brings the model structures with reference
and nsSNPs, template,
and protein sequence. You can test how Friend applet works. [Test
the applet]
Red vertical lines in the sequence indicates the location
of nsSNPs.
Red colored ball and stick display shows the location of both nsSNP
and reference SNP on the models.
Search StSNP by a protein sequence identification number
Protein search is done by entering a NCBI's protein accesion id (Ex:
NP_000843).
This query will present available nsSNPs links with the reference and
nonsynonymous amino acids for the protein of interest including the
link to the related chromosome.
If modeling is available, the template for modeling nsSNPs onto protein
structures will be shown.
The resulting report pages provide the user with options for modeling,
which is dependent upon two criteria: (1)the nsSNP(s) has to be within
the alignment of the protein sequence with template
(2) the sequence identity of the alignment has to be >= 30%.
Search will provide a link to pathway information if the data is available.
PDB search is done by entering a PDB id (Ex: 1att).
This query will bring all available proteins that are aligned with structures
for modeling option.
You will find the % sequence similarity between templates and protein
sequences including the available nsSNPS locations in the alignment.
If modeling is available, a button will be seen on the side of the alignment
to send the chosen alignment.
Search will also provide a link to pathway information if the data is available.
Search StSNP by by a keyword or full name of the protein
Entering a keyword starts the search, it will bring the possible hits with full protein name and link to which includes protein, nsSNP, template for modeling option and the pathway information if it is available.
NCBI's rs_number entry starts the search. Query for rsnumber search should be done by entering only the number portion of rs_number (Ex: 11553892)
This query will bring chromosome number of the nsSNPs that belongst to, protein accesion id with a link to StSNP, definition of the protein, residues for nsSNP and referenceSNP, position of the nsSNP on the protein sequence, and all homologous structures that are available.
When it is clicked on "Homologous Structures are available " link, this will bring a list of PDBs which are linked to StSNP for more search other nsSNPs and aligments.
Search nsSNPs within metabolic pathways When the pathway is chosen from the drop down menu. This will bring the pathway picture with a list of members exist in the pathway. Below the pathway picture, a table shows gene name, gene description, and EC number. Every gene in the row has a link
If there are any nsSNPs with the chosen gene this will give new options to search at StSNP for the next step.
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StSNP to search nsSNPs, protein sequences, and templates for modeling.
Search gene for nsSNPs and protein
Gene search is done by entering a gene name (Ex: ACAD).
This query will bring available nsSNPs links with the reference and nonsynonymous
amino acids for the gene of interest including the link to the related
chromosome.
If modeling is available, the template for modeling nsSNPs onto protein
structures will be shown.
The resulting report pages provide the user with options for modeling,
which is dependent upon two criteria: (1)the nsSNP(s) has to be within
the alignment of the protein sequence with template
(2) the sequence identity of the alignment has to be >= 30%.
Search will provide a link to pathway information if the data is available.
Top 500 proteins that have the most number of nsSNPs
This query will bring the information as the title says "Top 500 proteins that have the most number of nsSNPs"
If the homologues structures are available then there will be a link to search all available structures for nsSNPs at StSNP. Also protein accesion button will start a search in StSNP.
Get proteins according to their length and % similarity with available structures
Query is created by choosing the protein length and % similarity of
protein sequence with available structures. Search will bring two main
links: protein sequence with the desired length and protein structure
with chosen % similarity.
From this point by using either of them a new search starts at StSNP
to find available nsSNPS.
Get proteins with following substutions
In this query from the drop down menu residue 1 and residue2 are chosen, respectively which represents the reference SNP and nsSNP by also choosing the chromose location.
If the chosen composition brings any data, this will consist all available proteins with these specific configuration of reference and nsSNPs Search can be continued by choosing protein from the presented list to create a new query at StSNP.