GTEx Tissue Image Library

The GTEx Histological Image Viewer contains detailed tissue histology images collected from approximately 40 different tissue types from nearly 1000 postmortem donors as part of the Genotype-Tissue Expression (GTEx) program. All tissues underwent stringent pathology review for tissue acceptability and each file contains details including the type of fixative, the degree of autolysis, as well as age range and gender. Additionally, the high resolution of each image allows for detailed viewing including pan, and zoom. For your convenience, files can be downloaded as Aperio image files for further analysis.

Visit the GTEx Tissue Image Library

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How to keep chain ID / IDs in GROMACS?

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 ]

Python : Turtle tree

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() ===========...

How to use MODELLER to build DIMER homology model with ligand?

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, ...

Plagarism Checker

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

Homology model validation

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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