More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

http://molbiolabccsumrt.webs.com/

Applications are invited for one post of RA in a DBT funded research project “Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) Scheme of BTISet”.

Candidate should have a Ph.D. degree in Bioinformatics/Biotechnology/Genetics and Plant Breeding with adequate experience in the area of Bioinformatics. If a suitable candidate for the post of RA is not available, a JRF/SRF may be appointed.

Candidate for the post of JRF/SRF should have Master’s degree in relevant subject with adequate experience in the area of Bioinformatics and should be NET/DBT-BINC qualified

Interested candidates may send their bio-data to Prof. H. S. Balyan (hsbalyan@gmail.com) (in exceptional case, bio-data may also be submitted at the time of interview) and attend the interview on Monday, March 30, 2015 at 11:00 AM in the Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut. Candidates shall bring their original documents at the time of interview for verification. No interview letters will be issued and no TA/DA will be paid.

Address of the bookmark: http://christophergandrud.github.io/d3Network/

Code in almost all popular languages using Coding Ground. Edit, compile, execute and share your projects, 100% cloud.

http://www.tutorialspoint.com/codingground.htm

Address of the bookmark: http://www.tutorialspoint.com/codingground.htm

3D-Dock Suite

Global rigid search: FFTShape complementarity and electrostatics

Re-scoring and clustering. Refinement of interface side-chains

3D-Garden

Global rigid search in ensamble

Shape complementarity and Lennard–Jones potential

Side chain and backbone dihedral refinement

DOT

Global rigid search: FFTShape complementarity, electrostatics and VDWNone

Escher NG

Global rigid searchShape complementarity, hydrogen bonds and electrostatic

Integrated in VEGA

GRAMM 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potential

Clustering of conformations

GRAMM-X 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potentialminimization and re-scoring with multiple filters

HEX

Global rigid search: Fourier correlation of spherical harmonics

Shape complementarity

HADDOCK

Global rigid searchElectrostatic ,VDW and desolvation energy termsMD simulated annealing refinement . Filtering based on external data. 

ICM

Global rigid search: Monte CarloEmpirical scoring function

Clustering and selection of conformations. Refinement of interface side-chains and re-scoring

MolFit 

Global rigid search: FFTShape complementarity

Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations

PatchDock

Global rigid searchShape complementarity and atomic desolvation energy

Clustering of conformations

PyDock

Global rigid search:FFTShape complementarity

rescoring by binding electrostatics and desolvation energy

RosettaDock

Local rigid search: Monte Carlo with low and high resolution structure representation levels

Different scoring parameters for the different resolutions 

ZDOCK

Global rigid search: FFTShape complementarity, desolvation energy, and electrostatics.

Energy minimization and re-scoringFree for academics

Point to note:

The proper treatment of flexibility in protein–protein docking is still an active field of research. You first should analyzed your proteins in order to define their conformational space and then choose the most suitable method for your docking problem.

DEPARTMENT OF BIOTECHNOLOGY

No. NITW/Bio/ Date: 30th March 2015

ADVERTISEMENT FOR PROJECT FELLOW (Research Staff)

Applications are invited for the post of Project Fellow (Research Staff) for the project entitled ‘Metagenome derived nitroreductases for degradation of nitro compounds’ sponsored by the Department of Science and Technology (DST-INSPIRE), Govt. of India.

Position: Project Fellow (1 No.)

Project Duration: 5 years

Note: The post is purely on temporary basis for a period one year and may be extendable till the end of the project based on the progress of the candidate.

Emoluments: Rs. 14,000/- per month (Consolidated) for first two years and Rs. 16,000/- per month (Consolidated) for next three years.

Essential Qualifications:

i) First class in M.Tech/M.S (Biotechnology/Industrial Biotechnology/Bioinformatics) or equivalent. Or

ii) First class in M.Sc. (Biotechnology/Bioinformatics/Biochemistry/ Microbiology/Molecular biology).

Desirable Qualification: Preference will be given to candidates who have cleared NET/GATE or having prior work experience in Molecular biology/Bioinformatics sequence analysis.

Interested candidates may submit their application in plain paper along with Curriculum Vitae and photocopies of certificates in support of educational/professional qualifications. Application should be sent in a closed cover with a superscription on the cover “Application for the post of project fellow (DST-INSPIRE)” on or before 20.04.2015 (Monday) via Post to the Principal Investigator. Eligible candidates will be intimated through e-mail and called for interview at the Department of Biotechnology, NIT, Warangal. No TA/DA will be paid for attending the interview. Dr. K. Divakar (Principal Investigator) DST-INSPIRE Faculty Department of Biotechnology National Institute of Technology Warangal – 506 004. Telangana, India. E-mail: divakar@nitw.ac.in; kdivak@gmail.com

Advertisement: http://www.nitw.ac.in/nitw/announcements/2015/Notification_Project_Fellow_DST_INSPIRE_Biotechnology_NITW.pdf

Download 

http://arthropods.eugenes.org/EvidentialGene/trassembly.html

https://sourceforge.net/p/evidentialgene/blog/

Address of the bookmark: http://arthropods.eugenes.org/EvidentialGene/trassembly.html

The engagement is purely temporary on contractual basis and co-terminus with the project. There will be no provision of absorption of absorption/reemployment in IVRI/DBT on termination of the project.

No TA/DA will be provided for appearing in the interview and no separate letter will be issued.

A. Name tile of the project: “Centre for Agricultural bioinformatics (CABin)”.

B. Position/post to be filled: Research Associate (one)

C. Essential/Desirable qualifications:

•Essential: M.V.Sc./M.Tech./MSc Degree in Biotechnology/ Biochemistry/ Microbiology/Immunology/Bioinformatics/Genetics/Life Sciences or

Masters in Computer Application/ Masters in Computer science with first division.

• Desirable: Experience in cell culture, next generation sequencing, C++ and perl programming. NET/GATE qualified will be preferred.

• Experience : At least 2 years

D. Emoluments: Rs. 23000/- per month + 20% HRA

E. Age Limit: Maximum 40 years for men and 45 years for women

F. Duration of the project: Up to March 2017

G. Name of PI/Contact person: Dr. G.V.P.P.S. Ravi Kumar, Sr. Scientist, Division of Veterinary Biotechnology.

H. Address for correspondence: Dr. G.V.P.P.S. Ravi Kumar, Sr. Scientist, Computational Biology and Genomics facility,Division of Veterinary Biotechnology, I.V.R.I., Izatnagar – 243122

Advertisement: www.ivri.nic.in/jobs/WalkIn_interview_01042015.pdf

CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)

CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)

Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal

NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/

Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html

SILVA - https://www.arb-silva.de/

RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)

1. “Development of bioinformatics methods for identifying novel secondary metabolites by genome mining” funded by DBT

JRF (P)/SRF (P) (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: JRF (Project): M.Sc (Bioinformatics/ Biophysics/Biotechnology or any other stream of biological/physical sciences) or M.Tech. (Bioinformatics/Biotechnology/Computational Sciences) of M. Pharm.

SRF (Project): M.Sc (Bioinformatics/Biophysics/Biotechnology or any other stream of biological/physical sciences) or M.Tech. (Bioinformatics/Biotechnology/Computational Sciences) of M. Pharm with atleast 03 years of research experience.

Desirable Qualifications: Strong computer programming skills (in PERL/CGI/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment) and sufficient experience in computational analysis of biological/biochemical data.

The candidates must highlight their experience in programming and database development in their CV. Job description: Computational analysis of genomes and development of bioinformatics tools and software’s for sequence and structure based analysis of biosynthetic pathways.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience JRF (Project): Rs. 12,000/- per month plus 30% HRA SRF (Project): Rs. 14,000/- per month plus 30% HRA (*Candidates possessing qualifications as per latest DST OM, will be given revised scales).

More at http://www1.nii.res.in/sites/default/files/projectappointments-Dr.DebasisaMohanty-30April2015.pdf