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DOAJ (Directory of Open Access Journals)

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DOAJ (Directory of Open Access Journals)

DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals. DOAJ is independent. All funding is via donations, 40% of which comes from sponsors and 60% from members and publisher members. All DOAJ services are free of charge including being indexed in DOAJ. All data is freely available.
DOAJ operates an education and outreach program across the globe, focussing on improving the quality of applications submitted.

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Journals and their articles are categorised using a subset of the Library of Congress Classification. You can either type a keyword into the box below or click the arrows in the tree to expand and collapse subjects. Clicking on a subject will reveal the number of available records in the box on the right.

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How to keep chain ID / IDs in GROMACS?

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In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f  xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]
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Python : Turtle tree

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Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========...
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How to use MODELLER to build DIMER homology model with ligand?

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How to use MODELLER to build DIMER homology model with ligand? Procedure:     Get Fasta sequence from UNIPROT database.     Predict sequence alignment from HHPRED     Prepare INPUT files for MODELLER     model-dimer.py (Click to download) ############### from modeller import * from modeller.automodel import * #from modeller import soap_protein_od env = environ() env.io.hetatm = True a = automodel(env, alnfile='TvLDH-1bdm.ali',               knowns='1bdm',               sequence='TvLDH',               assess_methods=(assess.DOPE,                            ...
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Plagarism Checker

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Plagiarism is a serious academic misconduct. Whether you are a student writing a college essay, a teacher reviewing a student’s submission, or just someone who works extensively with content, it is important to ensure that the content is not plagiarized. Following are some resources to check Plagiarism. http://www.plagscan.com https://www.plagramme.com/   http://www.plagiarisma.net/fr/# http://www.scanmyessay.com http://www.plagtracker.com http://www.duplichecker.com http://www.smallseotools.com/plagiarism-checker http://www.plagium.com/fr/detecteurdeplagiat http://www.paperrater.com/plagiarism_checker http://www.copyleaks.com http://www.plagiarismchecker.com http://www.quetext.com http://plagiarismdetector.net http://www.solidseotools.com/plagiarism-checker http://www.dustball.com/cs/plagiarism.checker http://www.articlechecker.com http://www.plagiarismcheck.org
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Homology model validation

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Homology model can be validated in multiple ways. Here you will find useful description on how to validate your homology model. Web-servers: UCLA-DOE LAB — SAVES : The Structure Analysis and Verification Server ( New Link ) This metaserver runs 6 programs for checking and validating protein structures during and after model refinement. PROCHECK : Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. WHAT_CHECK : Derived from a subset of protein verification tools from the WHATIF program (Vriend, 1990), this does extensive checking of many sterochemical parameters of the residues in the model.   ERRAT : Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures.   VERIFY_3D : Determines the ...
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