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Molecular Mechanics Poisson-Boltzmann Surface Area on Cloud Computing
Following our widely explored repository “ 𝗠𝗼𝗹𝗲𝗰𝘂𝗹𝗮𝗿 𝗗𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗼𝗻 𝗖𝗹𝗼𝘂𝗱 𝗖𝗼𝗺𝗽𝘂𝘁𝗶𝗻𝗴 ” and its pre-print, we’re introducing a workflow designed for Google Colab and HPC/Jupyter systems (environments without a GUI) to run GMX_MMPBSA ( 𝙈𝙤𝙡𝙚𝙘𝙪𝙡𝙖𝙧 𝙈𝙚𝙘𝙝𝙖𝙣𝙞𝙘𝙨 𝙋𝙤𝙞𝙨𝙨𝙤𝙣–𝘽𝙤𝙡𝙩𝙯𝙢𝙖𝙣𝙣 𝙎𝙪𝙧𝙛𝙖𝙘𝙚 𝘼𝙧𝙚𝙖 )! Molecular dynamics (MD) simulations help us see how biological molecules behave in motion, revealing mechanisms behind

Taner Karagol
Oct 181 min read


When Half a Protein Is Enough!
In the world of membrane proteins, truncated isoforms have long been treated as evolutionary leftovers - partial gene products that don’t quite “make the cut”. In many studies, they are filtered out of analyses as unstable, nonfunctional, or even nuisances. We too once viewed them this way. For this interesting behind the paper story, you can check our article in Springer Nature: https://go.nature.com/483kVvV

Taner Karagol
Oct 181 min read


What Do Membrane Proteins Really Want? (Behind the Paper)
To check our interesting behind the paper story, please visit: https://go.nature.com/3KnbhdB

Taner Karagol
Oct 181 min read


Turning Ideas Into Patents: Lessons Learned & Challenges
Many people assume that innovation in medicine must start within the walls of a university. However, my experience has been quite the...

Taner Karagol
Feb 121 min read


Biology meets economics: game theory and medicine
Biology and economics are often viewed as separate domains, but they share a surprising connection on principles like game theory and...

Taner Karagol
Jan 32 min read


The "Science Side" of London
During my long stay in London, I discovered a thriving science scene that might not be immediately apparent to everyone. This city, known...

Taner Karagol
Jul 10, 20241 min read


Molecular Dynamics on Google Compute Engine, AWS (Amazon Web Services), and other Cloud Computing services
New Update: This project is now accompanied by a published paper on bioRxiv, which benchmarks molecular dynamics simulations across...

Taner Karagol
Feb 29, 20242 min read


HGVS Missense Variants to FASTA format Converter
Are you a researcher working with protein sequences? If so, you know the importance of accurately studying the effects of missense...

Taner Karagol
Feb 23, 20242 min read


Stargazing for Beginners: A Guide to Using Your Basic Space Telescope
Embarking on a celestial adventure with your very first telescope is an exciting endeavor. If you're ready to gaze into the cosmos,...

Taner Karagol
Jan 2, 20242 min read
Decoding Genomic Language: Polymorphism, Mutation, and Variant
The term "mutation" was used for either a generic alteration or, more specifically, a change with disease implications. Also, the term "polymorphism" was used to explain those genetic alterations occurring at a frequency of 1% or higher. However, this dual usage has led to confusion and misinterpretation across various disciplines. To solve this problem, a shift away from the terms "mutation" and "polymorphism" has been adopted. Instead, a preference is given to using neutr

Taner Karagol
Jan 2, 20241 min read
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