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Showing posts with label pdb. Show all posts
Showing posts with label pdb. Show all posts
Wednesday, January 12, 2011
Saturday, November 27, 2010
Rasmol Tool:
8:19 AM
GCbioinfo
RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s get started this useful tool Download Rasmol
here. Install Rasmol to your system and get started.
here. Install Rasmol to your system and get started.
Tuesday, November 2, 2010
primary structure analysis:
8:11 AM
GCbioinfo
Tool:
Radar:De novo repeat detection in protein sequences
I entered the protein albumin in uniprot and get the following result It gave the number of repeats present in the sequence.
http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/radar/radar-20101102-1505421645.html
Radar:De novo repeat detection in protein sequences
I entered the protein albumin in uniprot and get the following result It gave the number of repeats present in the sequence.
http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/radar/radar-20101102-1505421645.html
Monday, November 1, 2010
primary structure analysis:
7:39 AM
GCbioinfo
Tools:
HeliQuest A web server to screen sequences with specific alpha-helical properties HeliQuest calculates from an α-helix sequence its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
The server is divided into 2 interconnected modules: the sequence analysis module and the screening module.
In addition, the mutation module, (available from the sequence analysis module), allows user to mutate helices manually or automatically by genetic algorithm to create analogues with specific properties.-http://heliquest.ipmc.cnrs.fr/
After entering the helix sequence of the protein this protein sequence is get by entering the name of the protein in uniprot then paste it by clicking the analysis button and get the following
http://heliquest.ipmc.cnrs.fr/cgi-bin/ComputParams.py
HeliQuest A web server to screen sequences with specific alpha-helical properties HeliQuest calculates from an α-helix sequence its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
The server is divided into 2 interconnected modules: the sequence analysis module and the screening module.
In addition, the mutation module, (available from the sequence analysis module), allows user to mutate helices manually or automatically by genetic algorithm to create analogues with specific properties.-http://heliquest.ipmc.cnrs.fr/
http://heliquest.ipmc.cnrs.fr/cgi-bin/ComputParams.py
7:19 AM
GCbioinfo
Tools:
ScanSite pI/Mw:Compute the theoretical pI and Mw, and multiple phosphorylation states. Enter a protein name and sequence below. The molecular weight and isoelectric point of this sequence and multiple phosphorylation states will be displayed. http://scansite.mit.edu/calc_mw_pi.html
out put will be
ScanSite pI/Mw:Compute the theoretical pI and Mw, and multiple phosphorylation states. Enter a protein name and sequence below. The molecular weight and isoelectric point of this sequence and multiple phosphorylation states will be displayed. http://scansite.mit.edu/calc_mw_pi.html
out put will be
primary structure analysis 3:
7:06 AM
GCbioinfo
Tool:
Compute pI/Mw: Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
now go to this tool and get the required result Please enter one or more UniProtKB/Swiss-Prot protein identifiers (ID) (e.g. ALBU_HUMAN) or UniProt Knowledgebase accession numbers (AC) (e.g. P04406), separated by spaces, tabs or newlines. Alternatively, enter a protein sequence in single letter code. The theoretical pI and Mw (molecular weight) will then be computed. previosly I entered the amino acid sequence and now I am going to enter the uniprot AC#.http://www.expasy.org/cgi-bin/pi_tool
it will give you this format of result so click on the following things according to the instructions mentioned Please select one of the following features by clicking on a pair of endpoints, and the computation will be carried out for the corresponding sequence fragment.
Compute pI/Mw: Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
now go to this tool and get the required result Please enter one or more UniProtKB/Swiss-Prot protein identifiers (ID) (e.g. ALBU_HUMAN) or UniProt Knowledgebase accession numbers (AC) (e.g. P04406), separated by spaces, tabs or newlines. Alternatively, enter a protein sequence in single letter code. The theoretical pI and Mw (molecular weight) will then be computed. previosly I entered the amino acid sequence and now I am going to enter the uniprot AC#.http://www.expasy.org/cgi-bin/pi_tool
it will give you this format of result so click on the following things according to the instructions mentioned Please select one of the following features by clicking on a pair of endpoints, and the computation will be carried out for the corresponding sequence fragment.
Primary structure analysis 2:
6:51 AM
GCbioinfo
Tool :
ProtParam :Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
First go to this page http://www.expasy.org/tools/ select Primary structure analysis and select the first tool as I mentioned. click the tool and I entered the amino acid sequence of protein transgelin-2 in http://www.expasy.org/tools/protparam.html then get the out put page
http://www.expasy.org/cgi-bin/protparam
the out put is
ProtParam :Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
First go to this page http://www.expasy.org/tools/ select Primary structure analysis and select the first tool as I mentioned. click the tool and I entered the amino acid sequence of protein transgelin-2 in http://www.expasy.org/tools/protparam.html then get the out put page
http://www.expasy.org/cgi-bin/protparam
the out put is
Primary structure analysis:
6:36 AM
GCbioinfo
Now we are going to the expasy server for the Primary structure analysis of proteins by using different tools available at expasy server.
I will breifly tell you how to use these tools.
I will breifly tell you how to use these tools.
Saturday, October 30, 2010
PDB structures part 3
8:27 AM
GCbioinfo
The previous page contains the PDB ID of the particular protein
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=34605
get this PDB ID and entered into PDB and get the same 3D structure of the protein
http://www.rcsb.org/pdb/explore/explore.do?structureId=1WYM
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=34605
get this PDB ID and entered into PDB and get the same 3D structure of the protein
http://www.rcsb.org/pdb/explore/explore.do?structureId=1WYM
PDB structures part 2
8:18 AM
GCbioinfo
As we entered the gene name to ncbi and get complete information about the gene and also get the protein which is encoded by the gene. Get this name and entered into the structure database in ncbi. http://www.ncbi.nlm.nih.gov/sites/structure/?term=Transgelin-2
the protein entered is Transgelin-2
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=34605
view 3D structure using cn3d which is a structure viewer I mentioned in my very previous tutorial how to use and download cn3d 4.0 to your systems
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=34605
view 3D structure using cn3d which is a structure viewer I mentioned in my very previous tutorial how to use and download cn3d 4.0 to your systems
3.PDB:
4:27 AM
GCbioinfo
PDB is a protein data bank it contains information about the structure and function of the reported proteins. Not only the information about the protein is present but also of many macromolecules like nucleic acids and carbohydrates.
How to Search PDB:
go to http://www.rcsb.org/pdb/explore/motm.do
enter PDB ID if you don't know the ID then enter the text methylenetetrahydrofolate reductase to get the structural information of that protein
I entered this text then get this result go to this page http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=FA02BFE5&tabtoshow=Current
How to Search PDB:
go to http://www.rcsb.org/pdb/explore/motm.do
enter PDB ID if you don't know the ID then enter the text methylenetetrahydrofolate reductase to get the structural information of that protein
I entered this text then get this result go to this page http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=FA02BFE5&tabtoshow=Current
