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The Email That Made My Coffee Go Cold
Big news: I'm joining MIT as a Novo Nordisk Fellow, and I'll be doing my postdoc at L4TE. There are emails you skim, emails you archive, and emails you read four times in a row while your coffee quietly goes cold. Not long ago, I got one of the last kind. It said I'd been selected as an MIT–Novo Nordisk AI Postdoctoral Fellow, and that I'll be carrying out my postdoctoral research at MIT in L4TE, Giovanni Traverso's Laboratory for Translational Engineering. technologyreview T
Alper KARAGÖL
Sep 242 min read
Karagol-Ramachandran Plots: Extending Conformational Analysis Beyond the Carbon World
When carbon gives way to silicon, the classic conformational analysis tools fall silent. Here is how we adapted one of structural biology's most iconic plots for a new class of polymers — and packaged it for anyone to use. The Ramachandran plot has guided structural biology for over sixty years. By mapping the two backbone dihedral angles φ and ψ for every residue in a protein, it reveals at a glance whether a structure is sterically plausible, which secondary structures are
Alper KARAGÖL
Mar 113 min read
Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA): A Physics-Based Perspective on Binding Free Energy
At its core, MM-PBSA is a framework for estimating the thermodynamic potential of molecular association, grounded in the canonical ensemble of statistical mechanics. The binding of a ligand (L) to a receptor (R) to form a complex (RL) can be rigorously described by the Helmholtz free energy difference: ΔG_bind = G_RL - (G_R + G_L) = -k_B T ln(Z_RL / (Z_R Z_L)), where each Z is a configurational partition function integrating over all atomic coordinates and solvent degrees of
Alper KARAGÖL
Oct 18, 20253 min read
Timing Is Everything: How I Learned to Avoid Bench Rejection and Choose the Right Journal
When I first started submitting my research, I thought the hard part was writing the manuscript. I’d finish my draft, do a quick...
Alper KARAGÖL
Aug 16, 20253 min read
Optimizing Early Research Resource Allocation
Resource allocation in the early stages of research is a critical factor that can determine the success or failure of a project. Whether...
Alper KARAGÖL
Feb 3, 20252 min read
Observing Then Hypothesis vs. Hypothesis Then Observing: Which is Better and Less Biased?
In the world of scientific inquiry and research, one of the most fundamental questions revolves around the methodology used to explore...
Alper KARAGÖL
Jun 5, 20242 min read
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