Bioinformatics Today

Molecular Dynamics Simulation Steps Gromacs software

2026-04-19T21:48:00.000-07:00

Molecular Dynamics Simulation using Gromacs software

Here, For the protein pdb 1AKI, MD simulation has to be run for 1 nanosecond in water as a solvent

Install Gromacs in Ubuntu Linux: type the command: "sudo apt-get install gromacs" in command terminal

keep your PDB file in a new folder create in Desktop. Now in command terminal type: "ls"
check that your location is correct or not. If not, go to your folder location containing pdb file by typing "cd .."

Then type the following commands

Step 1: pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce -ignh

opls force field (5)

editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.8 -bt cubic

genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr

genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 8

grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr

mdrun -v -deffnm em

grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr

mdrun -deffnm nvt

grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -o npt.tpr

mdrun -deffnm npt

grompp -f md.mdp -c npt.gro -t npt.trr -e npt.edr -p topol.top -o md_0_1.tpr

mdrun -deffnm md_0_1

Job vacancy for Bioinformatics and Lifesciences 2011

2011-08-27T04:43:00.000-07:00

Excellent opening for Grant Proposal & Publication Writers at Genome Life Sciences

Responsibilities : Identifying potential grant funding agencies, grant proposal writing, interacting and liaisoning with scientists, preparing and presenting scientific content, submitting proposals to domestic/international agencies, resource planning, requirements analysis, and events management; writing and co-ordinating research publications with scientists.
Experience : 4-7 years
Location : Chennai
Education : B.Sc - Life Science | M.Sc - Life Science
Contact Details :
Genome Life Sciences
Website : http://www.genome.com
Executive Name : Vinoth Sankaran
Address : Genome lifesciences pvt ltd
3rd floor, Dev's Ark, #284/1B, OMR,
Kottivakkam
CHENNAI,Tamilnadu,India 600096
Email Address : careers@genome.com
Telephone : 91-44-24540498
Deadline : 25.09.2011

Importance of computer knowledge in Biology

2011-08-10T23:56:00.000-07:00

Read an interesting article posted in Nature's blog highlighting that how a computer knowledge or computational
biology makes microorganism essential for environmental cleaning

Click here

Installing AutoDock in Ubuntu Linux Easy steps

2011-08-07T23:16:00.000-07:00

Step by step Installation of AutoDock MGL-Tool on Ubuntu Linux

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 press Next, Next, Finish

List of companies offering jobs in Bioinformatics India

2011-08-02T00:07:00.000-07:00

The following companies offering jobs for Bioinformatics graduates in India

Company Name                                  Location

GVK BioSciences Pvt. Ltd                   Hyderabad
Strand Genomics                                   Bangalore
AstraZeneca                                          Bangalore
Dr Reddy’s Laboratories                       Hyderabad
Ingenovis (division of I labs)                   Hyderabad
Jubilant Biosys (subsidiary from
Jubilant Organosys)                                Noida, UP
Landsky Solutions                                  Secunderabad
Molecular Connections                           Bangalore
Ocimum Biosolutions                              Hyderabad
PrayogNET Computing                          Chennai
Questar Bioinformatics                           Hyderabad
Satyam Computers                                 Hyderabad
Spectramind Services                             New Delhi
Total Consultancy Services                     Hyderabad

Job vacancy for Bioinformatics

2011-08-02T00:02:00.000-07:00

C-DAC Pune offers project engineering jobs for Bioinformatics graduates

Name of the Post    Position Code     No. of Positions
Project Engineer     PNE/BIO-PE-1/117     3
Project Engineer     PNE/BIO-PE-2/117     1
Project Engineer     PNE/BIO-PE-3/117     1

Apply online

Job vacancy for Bioinformatics

2011-07-20T01:41:00.000-07:00

Applications on plain paper are invited having full details about educational qualifications and experience etc, all relevant certificates / markssheets / documents and a DD of Rs 300/- in favour of Head, School of Biotechnology, DAVV, Indore payable at Indore for 9 vacant posts of contractual lecturers in Bioinformatics, Genetic Engineering, Biotechnology, Number of posts may vary.

Post : Lecturer
No of Posts : Nine
Stream : Bioinformatics
Salary : Consolidated salary and amount depending on qualification and experience
Venue :
Devi Ahilya University
School of Biotechnology
Khandwa Road, Indore - 452001
Date of Interview : August 12, 2011 at 10.30 AM in the School of Biotechnology. No separate letter will be issued for interview. No TA/DA will be paid for attending interview.

Deadline : 06.08.2011

Apply soon: http://www.dauniv.ac.in/notices/Employment%20Notice.pdf

Ph.D position in Bioinformatics

2011-07-16T00:08:00.000-07:00

Ph.D position at Sperling Lab, Max Planck Institute of Molecular Genetics, Berlin,

Germany

Qualifications:
- University degree in bioinformatics or an equivalent university degree in natural science
- Excellent knowledge in statistics and programming languages (R, Perl, Java)
- Database administration and handling skills are a plus
- Excellent verbal and written English communication skills are required
- Candidates should be strongly motivated, team-oriented and should have the ability to work
independently
The position will be granted for an initial period of 3 years with a salary up to 13/2 TVöD depending on
the qualification of the applicant.

Apply soon:http://www.molgen.mpg.de/~heart/openposition.htm

Job vacancy for Bioinformatics and Lifesciences

2011-07-06T20:27:00.000-07:00

Parthys
Reverse Informatics
The Art of Generating New Knowledge North Phase Developed Plots
Guindy Industrial Estate
Ekkaduthangal, Chennai 600 032
India
Landmark: Opp. to Jaya TV Office
T: +91-44-4261-7070
F: +91-44-4264-7141
M:+91-95000-41131

Position: Research Associate:

Job Code: LIFE
Qualification: M.Sc - Bio-Technology/Bio-Informatics/Bio-Chemistry
Good analytical skills
Knowledge in Genetics and Pharmacology is an added advantage

Send your resume to : careers@reverseinformatics.com

Apply soon

Bioinformatics Courses in India

2011-06-16T04:19:00.000-07:00

Bioinformatics

List of Educational Institutes in India

Overview of the course

It is fast emerging interdisciplinary research area. It gives the opportunity to quickly and efficiently study heap of genetic sequences, chemical structure and other biological data and to use these databases to solve various problems and mysteries and uncover the wealth of the hidden biological information to enhance the standard of life for mankind. Bioinformatics has already started showing its profound impact on human health, agriculture, environment and energy. It is being used in the areas of molecular medicine to help produce better and more customized medicines to prevent or cure diseases, it has environmental benefit in identifying waste cleanup bacteria and in agriculture it can be used for producing high yield lows maintenance crops. The career prospects in the field have been steadily increasing with more and more use of information technology in the field of molecular biology.

Job prospects are in all sectors of biotechnology, pharmaceutical and biomedical sciences, in research institutions, hospital and industry. Challenges and career areas for any bioinformatician and bioinformaticist include sequence assembly, database design and information storage, management and integration, to develop sequence analysis software, proteomics (study 3D structure of protein and functions), gene mining, pharmacogenomics, informatics developer, biostatistics, computational chemist, bioanalytics and drug designing.

Cheminformatics is rapidly picking up the pace in India and foreign countries. Because of strong chemistry education sector with vast biochemical diversity along with well established ayurvedic system of medicine etc. India will be the hub of Cheminformatics very soon. Most of the patents for drugs are likely to expire around 2011. After that companies which will be having better drug discovery or Cheminformatics sector will concur the world drug market. With huge accumulation of gene and protein sequences database lots of career opportunities have opened in this field particularly in pharmacogenomics and gene chip designing.

Students with biosciences and chemistry in graduation and later learnt IT skills are now-a-days are eligible to apply in this field. But an IT person with strong knowledge of molecular biology is also preferred in bioinformatics.

Courses and Eligibility:

§ B.Tech in bioinformatics: 10 + 2 with Physics, Chemistry, Biology and English.

§ M.Sc in Bioinformatics: BSc/ BSc (agriculture)/BCS/Be/B.Tech/MBBS /B.Pharm/BHMS/BVSc.

§ Advanced diploma in Bioinformatics: M.Sc in Botany, Zoology, Life sciences, Biochemistry, Microbiology, Biotechnology, Biophysics, Pharmacology, Agriculture, or M.Tech or MBBS Physics, Chemistry, Mathematics and Computer sciences.

§ M.Tech in Bioinformatics: Pharmacy graduates, medical, dental and veterinary sciences and graduates or post graduates in science.

Educational Institutes

Amity University. www.amity.edu. Course: UG and PG courses in Bioinformatics

Best Biotek Research labs (p) Ltd. www.bestbiotek.com. Diploma in bioinformatics, Clinical and chem-informatics

Bharathiar university, school of biotechnology, Coimbatore– 641046, Tamil Nadu, phone- 0422-242222. Course: visit: www.bharathiaruniv.ac.in. Course:

Bioinformatics institute of India. Noida (UP). Course: PG/Advanced Diploma in Bioinformatics

Calcutta university, senate house, 87/1, college street, Kolkata- 700 073, phone- 0332241 0071. Web: www.caluniv.ac.in. Course:

Indian institute of information technology, Deoghat, Jhalwa campus, Allahabad- 211011, phone–91-532-2552380, web: www.iiita.ac.in. Course:

Infitech Global; Bangalore; Phone:93416 26309. www.infitechglobal.com. Course: PG diploma in bioinformatics.

Institute of bioinformatics and applied biotechnology, g-05, tech park mall, international technology park Bangalore (ITPB), Whitefield road, Bangalore – 560 066, phone- 91 (80) 2841 0029, 2841 2769, 2841 6034, web: www.ibab.ac.in. Course: Bioinformatics diploma and degree.

Institute of Bioinformatics and applied biotechnology. Joint venture of Karnataka govt and ICICI Bank; Offers PG Diploma in bioinformatics and 6-12 months lab course in Biotechniques.

Institute of Cheminformatics Studies, Noida. Course: Diploma in Cheminformatics. Department of Chemistry.

Jamia Hamdard Deemed University, New Delhi. Course: Diploma in Cheminformatics.

Jamia Millia Islamia university, department of computer science, Jamia nagar, new Delhi – 110 025, phone – 011-26980014, 26981717, web: www.jmi.nic.in. Course:

Jaypee institute of information technology university; Noida; www.jiit.ac.in. Bioinformatics

Karunya university, school of biotechnology, karunya nagar, Coimbatore–641114, Tamil Nadu, phone- 0422- 2614614. (5 lines), web- www.karunya.edu . Course:

Madurai kamaraj university, school of biotechnology, Madurai, Tamil Nadu, phone 0452-2459166, 2459455, web: www.mkuuniversity.org . Course:

Pondicherry university, bioinformatics centre, school of life sciences, Pondicherry- 605014. Web: www.bicpu.edu.in. Course:

SRM university, 3, Veera-Swamy street, west mambalam, Chennai–600 033. Phone–044-24742836, 24747231,
web: www.srm-univ.ac.in. Course:

The Indian institutes which offer training programme diploma courses include: Malabar Christian College, Kozikode. Course:1 Year P.G. Diploma in Cheminformatics, Eligibility: M.Sc. (Chemistry)/ M.Sc. (Bio-informatics)/ M.Pharma)

University of Hyderabad, Hyderabad, Andhra Pradesh, phone – 91-40-3010500, 23010245, web: www.uohyd.ernet.in. Course:

University of pune, the director, bioinformatics centre, Pune- 411 007, phone- 020-25692039, web: www.bioinfo.ernet.in. Course:

Homology modeling of protein using Modeller Software

2011-05-24T23:57:00.000-07:00

Homology modeling 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.

Career @ C-DAC pune

2011-05-18T23:32:00.000-07:00

C-DAC pune, requires Web Designers

C-DAC invites online applications from skilled and experienced professionals from the interdisciplinary domain of Information & Communication Technologies for the following areas of operations:

Apply Online

JRF position in BITS, Pilani Hydrabad campus

2011-05-02T04:25:00.000-07:00

BITS, Pilani Hydrabad campus requires M.Sc, M.Tech (completed or going to complete) Bioinformatics students for JRF post. Apply Soon: http://www.bits-hyderabad.ac.in/news_details.php?id=122

PhD position in Bioinformatics, University of Bern, Switzerland

2011-05-02T04:20:00.000-07:00

PhD position in Bioinformatics, University of Bern, Switzerland, Apply now through nature jobs: http://www.nature.com/naturejobs/science/jobs/192051-PhD-Student-Position-in-Bioinformatics-Structural-Computational-Biology-at-University-of-Bern

NIV, Pune requires Bioinformatician-Apply now

2011-05-02T04:10:00.000-07:00

NATIONAL INSTITUTE OF VIROLOGY, pune requires Technical Officer and Technical Assistant, Eligibility: Post Graduate in Bioinformatics, Apply soon: http://niv.co.in/New_vecancies/TECHNICAL%20POSTS-2010%20_03-03-2011.pdf

Phylogenetic Tree Construction using PHYLIP software

2011-05-02T00:04:00.000-07:00

Step1: Download and install Phylip software from http://evolution.genetics.washington.edu/phylip/getme.html

Step2: Do multiple sequence alignment of the sequence of interest using ClustalX software. In clustalx software, choose "save as phylip" option. After MSA, you will be saved three output file".aln", ".dnd", and ".phy" files.

Note: While doing clustalx, please note that the first header lines or organism names or protein names in fasta sequence file should be unique. If same or repetive names or gap between each fasta sequences occurs then clustalx will not run properly.

Step4: Copy ".phy file in C:/Program files/Phylip/exe/ folder

Step3: In C:/Program files/Phylip/exe/ folder, open bootstrap option. Now drag and drop"
".phy" phylip file, (calling it infile) Do 100 replicates. Give Random seed number: 3 (must be odd)
click Y to all the default parameters.

Step4. Open DnaDist (call infile, if you want, the previous outfile ) and change dataset as MULTIPLE DATASET, telling you did 100 replicates

Step5: Run neighbourjoining (call infile, if you want, the previous outfile ), and set multiple dataset to 100. you can set a root.

Now you have 100 trees in the outtree file.
you can already open this file with treeview, adding the extention .ph to the file.

Step6: Create a consensus tree: Run Consensus calling intree the outtree from NJ.

Step7. See the outtree.ph (i.e, fourth file that generated after running neighbourjoining) in Treeview.

Notes: in treeview from Tree Menu set: Internal edge label to see the bootstrap values.
The "real tree" is the first of the 100 created by NJ, the consensus tree is useful to know how reliable are the branches and the nodes.

Install AUTODOCK in Windows

2011-04-23T04:21:00.000-07:00

Installing AUTODOCK software in WINDOWS operating system

Step1: Download MGL Tools: http://mgltools.scripps.edu/downloads

Now, install MGL Tools by double click: Path should be in C:/Program Files

Step2: Download Autodock4 and Autogrid4 executable file from following link : http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/

After downloading, Double click the Autodock4.2.3_win32 executable file. Change the saving location to desktop: It will create a folder with a name " System32".

Inside the folder, you will be having three files "cygwin1.dll" , "autodock4.exe", "autogrid4.exe" . Now copy "cygwin1.dll file and paste it in C:/Windows/System32.

Next, copy the autodock4.exe and autogrid4.exe file and paste it in C:/Program Files/MGL Tools.

Now AUTODOCK is ready for working. Run autodock by clicking AutdockTools icon.

For working steps: see Autodock working steps post in this blog.

Careers @ Bioinformatics India

2011-04-23T03:31:00.000-07:00

Neugene Internationals Solutions, Pune looking for Bioinformatics Scientist
http://jobs.monsterindia.com/details/7692742.html?sig=js-1-54152a0048073011f552be3bfbefd57c-1&from=

Scigenome, Kerala
looking for Bioinformatics specialist
Apply online http://www.scigenom.com/aboutscigenom/careers.html

Strand LifeSciences, Bangalore
Need Bioinformatics specialist: http://www.strandls.com/Careers

DLI - Genetic Research and Development India, Hydrabad
Faculty Position in Bioinformatics: http://www.dnalabsindia.org/careers.php

AUTODOCK -protein ligand docking (Easy Steps) Running in WINDOWS

2011-04-18T05:54:00.000-07:00

AUTODOCK MANUAL FOR WINDOWS

(autodock –1.4 v, MGL Tool)

Protein: (Remove all hydrogen atoms manually before running)

File----- Read molecule----open “Protein.pdb”

Edit-----Hydrogen---Add---Polar only

Charges---add Kollman charges (e.g. -8.574)

File----save---write “protein.PDBQ”—click o.k

Ligand

Input----open “ligand.pdb”

Torsion tree---detect root

Output----save it a “ligand.PDBQT”

Grid

Macromolecule (protein)----Choose protein ---o.k---save it as “protein.PDBQT”

Set Map------directly---Accept

Grid box-----give X, Y, Z co-ordinates value (of active site from q-site finder server or from literature)

Grid Box

File----close saving current

Grid----output----save “protein.GPF”

Docking

Macromolecule----set rigid File name----open “protein.PDBQT”

Ligand------Choose----select a ligand----Accept

Docking-----search parameters----Genetic algorithm(GA)—Accept

Docking----other options---- choose AUTODOCK 4 parameter- Accept

Docking-----output(o/p)-----Lamarkian GA---save as protein.DPF

Run

Go to Run option

Run autogrid and then autodock (here change autogrid3 as autogrid4 and autodock3 as audodock4 while running autogrid and autodock.)
autogrid4 -p protein.gpf -l protein.glg
autodock4 -p protein.dpf -l protein.dlg

If you have problem during autogrid (Eg. Error such as “Cl.map file missing, then go to Grid option->edit GPF->rename C.map as Cl.map-Write it-Save and again run Autogrid.

Finally open DLG file through conformation option.

ANALYZING AUTODOCK RESULTS

STEP1. Load the docking solutions. Analyze --->Docking Logs --->Read Docking Log. (See page 27 of tutorial).

STEP 2. View the individual docking solutions. Analyze-->Conformations-->Show Conformations. You'll get a window, you can slide the slider through the 10 different solutions. You'll see each docking site separately. (see page 29 of tutorial).

STEP 3. View all the docked ligands at once to see how clustered the solutions are on the surface of the macromolecule. Analyze-->Molecules-->Visualize Dockings as Spheres. (see page 36 of tutorial).

STEP 4. To get the coordinates of docked ligand in PDB format, type get-docked macro_ligand.dlg. You'll get a pdb file with 10 docked ligands. You'll have to split the file into individual molecules yourself, if you want.