A weekly newsletter delivering the latest protein modeling tools and strategies to streamline your in silico processes, reduce wet lab workload, and save your organization time, effort, and resources.
Visualize binding pocket residues within 5Å of a ligand with PyMOL
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ProteinReach by Dr. Omar
A weekly newsletter delivering the latest protein modeling tools and strategies to streamline your in silico processes, reduce wet lab workload, and save your organization time, effort, and resources.
I always use MMGBSA and MMPBSA as initial binding energy methods. Then use free energy perturbation (FEP) method to assess how accurate my two initial measurements were. So, the sequence of usage goes like this: 1) MMGBSA2) MMPBSA3) FEP The only downside of using FEP is that is computationally expensive. And not many groups have the possibility of using that one. But if you do, please go ahead and use it. Thank you, Best, Omar. © ProteinReach|2026 SciLearningWorkshops LLC Unsubscribe ·...
During my PhD, I was lost in GROMACS MDS outputs. If you’re just getting started, that huge number of files can be overwhelming; I know that’s how I felt. To help with that, I put together a quick reference guide covering the most common GROMACS file extensions and what they do. Please save it and share it with a colleague who’s just starting with MD simulations! Thank you, Best, Omar. © ProteinReach|2026 SciLearningWorkshops LLC Unsubscribe · Preferences
I used Boltz-2 to predict the structure of a ligand-bound mutant protein complex (AtFAAH S305A bound to OdDHL) which I worked with during my PhD. The ligand, OdDHL, is a quorum sensing molecule. The crystal structure of this complex was previously resolved at 3.5 Å resolution, so not the highest quality.When comparing the predicted and experimental structures using the superimpose tool in PyMOL, I noticed that the Boltz-2 prediction successfully folds certain regions that were unresolved in...