#molecular modelling

[bpod-bpod]

Computer Virus

SARS-CoV-2 is the virus of the moment, but there’s a long list of ones that might jump from animals to humans and cause deadly outbreaks in the future. Thankfully, scientists are already investigating ways to treat and vaccinate should such an outbreak occur. Because the catalogues of viruses and candidate treatments are long, researchers use computers to lighten the load. Using molecular modelling software, they see which compounds are likely to interact with and inhibit a given virus, and can thus narrow the list of ones to test in the laboratory. The image shows a computer model of a Nipah virus protein (green) with a compound (purple) bound to the region responsible for infecting cells. Nipah viruses circulate in animals and rarely infect humans, but when they do it often has deadly consequences. With that in mind, it’s good to know scientists are already scanning the virus models for weaknesses.

Written by Ruth Williams

Image from the Southwest Research Institute

Southwest Research Institute, Texas Biomedical Research Institute, UT Health San Antonio, and The University of Texas at San Antonio

Image copyright held by Southwest Research Institute

From a Texas Biomedical Research Institute, press release, October 2021

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[ethicaledufabrica]

Edufabrica, Summer Training in Delhi NCR, Emerging Training Company, Winter Training, Technical Workshops in Delhi, Online Training Company

The hereditary information in humans and almost all other organisms is

deoxyribonucleic acid(DNA). Most of the parts of DNA are in the nucleus (nuclear DNA),

and a little amount of it is situated in mitochondria ( Mitochondrial DNA). It is the smallest genetic material of the human body and is very important. Its study is important for finding cures of genetic deformations, etc. It is formed from 2 polynucleotide chains the coil around each other in form of a double helix. This double helix carries the genetic information and instructions for the development, growth, functioning, growth, and reproduction of all organisms.

[magentatechnician]

What technicians do in their spare time

How to alleviate the boredom caused by COVID-19 lockdown: I’m having a go at knitting and crochet again. Here’s my attempt at modelling methane.

It’s going to take a lot more wool (and stuffing) to make some bigger molecules.

[ijtsrd]

Review on Computational Bioinformatics and Molecular Modelling Novel Tool for Drug Discovery

By Rishabh Jain "Review on Computational Bioinformatics and Molecular Modelling: Novel Tool for Drug Discovery"

Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-3 | Issue-1 , December 2018,

URL: http://www.ijtsrd.com/papers/ijtsrd18914.pdf

Direct URL: http://www.ijtsrd.com/pharmacy/pharmacoinformatics/18914/review-on-computational-bioinformatics-and-molecular-modelling-novel-tool-for-drug-discovery/rishabh-jain

technology journal, pharmacy journal, computer science journal

Advancement in science and technology has brought a remarkable change in the field of drug discovery. Earlier it was very difficult to predict the target for receptor but nowadays, it is easy and robust task to dock the target protein with ligand and binding affinity is calculated. Docking helps in the virtual screening of drug along with its hit identification. There are two approaches through which docking can be carried out, shape complementary and stimulation approach. There are many procedures involved in carrying out docking and all require different software's and algorithms. Molecular docking serves as a good platform to screen a large number of ligands and is useful in Drug-DNA studies. This review mainly focuses on the general idea of molecular docking and discusses its major applications, different types of interaction involved and types of docking.

[hisourart-blog]

[:en]CPK coloring[:]

[:en]In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. The scheme is named after the CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter Koltun.

History In 1952, Corey and Pauling published a description of space-filling models of proteins and other biomolecules that…

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[siliconandstardust]

When you ask your prof about a program and he gives you the install cd’s and the product keys...

Well, now I get to play with Gaussian. And so does everyone else.

[siliconandstardust]

Calculating the symmetries of the vibrational modes of cisplatin. Of course the next day in class we made a Maple file to do this, and now we’re working towards generalizing the file for all point groups/all molecules. 

It was still worth it to do the exercise by hand, though. For me, the hardest part of this exercise is the part that we still need to do by hand: placing the molecule in the coordinate system and determining the number of unshifted atoms for each symmetry operation.

[siliconandstardust]

This is my molecular modelling mess about half an hour into homework/practice problems. There was about an hour and a half after this, but by then I was way too involved in the work to even think about stopping to take pictures. Suffice it to say that there were modelling kit parts everywhere and my homework ended at 5 pages plus about 4 pages of scrap/abandoned approaches.

But still, this class is awesome, and totally worth the wait/trudge through thermodynamics, inorganic I, and quantum chemistry.