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Molecular Mechanics Poisson-Boltzmann Surface Area on Cloud Computing
Following our widely explored repository โ ๐ ๐ผ๐น๐ฒ๐ฐ๐๐น๐ฎ๐ฟ ๐๐๐ป๐ฎ๐บ๐ถ๐ฐ๐ ๐ผ๐ป ๐๐น๐ผ๐๐ฑ ๐๐ผ๐บ๐ฝ๐๐๐ถ๐ป๐ด โ and its pre-print, weโre introducing a workflow designed for Google Colab and HPC/Jupyter systems (environments without a GUI) to run GMX_MMPBSA ( ๐๐ค๐ก๐๐๐ช๐ก๐๐ง ๐๐๐๐๐๐ฃ๐๐๐จ ๐๐ค๐๐จ๐จ๐ค๐ฃโ๐ฝ๐ค๐ก๐ฉ๐ฏ๐ข๐๐ฃ๐ฃ ๐๐ช๐ง๐๐๐๐ ๐ผ๐ง๐๐ )! Molecular dynamics (MD) simulations help us see how biological molecules behave in motion, revealing mechanisms behind

Taner Karagol
Oct 18, 20251 min read
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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 donโt quite โmake the cutโ. 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 18, 20251 min read
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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 18, 20251 min read
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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 12, 20251 min read
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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 3, 20252 min read
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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
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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
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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
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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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