Tuesday, September 4, 2012

Major Biological Databases

Major Biological Databases Available Via the World Wide Web


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AceDB Genome database for Caenorhabditis elegans
www.acedb.org

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DDBJ Primary nucleotide sequence database in Japan
www.ddbj.nig.ac.jp

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EMBL Primary nucleotide sequence database in Europe
www.ebi.ac.uk/embl/index.html

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Entrez NCBI portal for a variety of biological databases
www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

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ExPASY Proteomics database
http://us.expasy.org

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FlyBase A database of the Drosophila genome
http://flybase.bio.indiana.edu/
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GenBank Primary nucleotide sequence database in NCBI
www.ncbi.nlm.nih.gov/Genbank

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HIV databases HIV sequence data and related immunologic information
www.hiv.lanl.gov/content/index

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Microarray gene expression database DNA microarray data and analysis tools
www.ebi.ac.uk/microarray

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OMIM Genetic information of human diseases
www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

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PIR Annotated protein sequences
http://pir.georgetown.edu/pirwww/pirhome3.shtml

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PubMed Biomedical literature information
www.ncbi.nlm.nih.gov/PubMed

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Ribosomal database project Ribosomal RNA sequences and phylogenetic trees derived from the sequences
http://rdp.cme.msu.edu/html

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SRS General sequence retrieval system
http://srs6.ebi.ac.uk

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SWISS-Prot Curated protein sequence database
www.ebi.ac.uk/swissprot/access.html

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TAIR Arabidopsis information database
www.arabidopsis.org

Sunday, September 2, 2012

Homology modeling of protein using Modeller Software


Step 1: Installing Modeller Software

Download and install latest version of  Modeller software:http://salilab.org/modeller/download_installation.html
After registration, you will get an academic licence for installation.

Step 2: Download and install python:http://www.python.org/download/releases/2.4/

Step 3: Paste your raw protein sequence and search against pdb database using BLASTP program

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
Note: Choose database search set as protein data bank (pdb). find the best template hit. The template hit should have atleast greater than 35% of identity. Note down the pdb id (Eg:1BDM).

Step 4: Now download the pdb file from pdb database:http://www.rcsb.org/pdb/home/home.do

Step 5: Go to C:\\Program Files\Modeller folder\

Now, copy the downloaded pdb file in modeller folder. Now rename the pdb file name as "1bdm.pdb"

Step 6: Now, open new notepad file, copy and paste the following program

>P1;TvLDH
sequence:TvLDH:::::::0.00: 0.00
MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPKA
AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPEN
FSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKKI
GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVV
EGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG*
Now, replace the existing sequence with your sequence. Only, sequence has to be replaced. Now, save the notepad file as "TvLDH.ali". Give the file name within the double quote.

Step 7: Now, open new notepad file, copy and paste the following program

from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb')
aln.append(file='TvLDH.ali', align_codes='TvLDH')
aln.align2d()
aln.write(file='TvLDH-1bdmA.ali', alignment_format='PIR')
aln.write(file='TvLDH-1bdmA.pap', alignment_format='PAP')
Now, save the notepad file as "align.py". Give the file name within the double quote. It will automatically changed into python format.
Now, run the "align.py" by double clicking it. It will run now and create 'TvLDH-1bdmA.ali' and 'TvLDH-1bdmA.pap' file. Depend on the sequence length, it will take time to complete.
Step 8: Now, open new notepad file, copy and paste the following program
from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='TvLDH-1bdmA.ali',
              knowns='1bdmA', sequence='TvLDH',
              assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()
Now, save the notepad file as "model.py". Give the file name within the double quote.
Run the "model.py" file by double clicking it. It will run and generate 5 pdb model.
Now check the model efficiency and accurecy by validating it. Go to SAVES server. http://nihserver.mbi.ucla.edu/SAVES/. upload the modelled pdb file, and run all the program.
Check the ramachandran plot value (should be greater than 95%) and errat value (should be great then 90%). If it is less, Do model optimization, energy minimization and protein (molecular dynamics) simulation.

Installing AutoDock in Ubuntu Linux Easy steps




Go to Command Prompt and type:  sudo apt-get install autodocktools
Go to http://autodock.scripps.edu/ and In download option, click ADT to dowload latest version of MGL-Tools downloads page.
After few seconds, It will ask Yes or No to install further, type yes.
Download file MGLTools-1.5.2-Linux-x86-Install to your home directory (e.g. /home/cepe/Desktop).
If you do not know where is your home directory,
Open terminal window by going to Applications --> Accessories --> Terminal; type cd ~ and press Enter; type pwd and press Enter; your home directory will be printed on the screen.
Open terminal window by going to Applications --> Accessories --> Terminal.
Type chmod +x MGLTools-1.5.2-Linux-x86-Install and press Enter.
Type ./MGLTools-1.5.2-Linux-x86-Install and press Enter.
An installation window should appear on the screen. Press Next, give yes, and pressNext, Next, Finish