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.
Am I the only one who sees a huge disconnect between protein designs and how efficiently they can be executed in the wet-lab? What do you think it’s missing?What could be done for it be improved? Are the datasets used to train those models not good enough anymore?What do you think? Best, Omar. © ProteinReach|2026 SciLearningWorkshops LLC Unsubscribe · Preferences
I came across a nanodisc-based purification approach that just changed how I think about membrane protein biochemistry. I wish I had known about this during my PhD.This approach, developed by Cube Biotech, allows the purification of membrane binding proteins without detergents. It relies instead on a copolymer based nanodisc technology.What makes this especially compelling is that the nanodiscs create an environment that closely resembles a native cell membrane.Here is what stood out to...
Do you struggle with assessing the movement of specific residues of your protein during MDS? Here, I have a tool that can help you with that……It’s called eRMSF, and it allows you to assess the movement of residues during molecular dynamics simulation (MDS) runs at specific time points. So no need to rely on average values in a traditional RMSF plot, instead, you can complement that with eRMSF. You’ll be able to have a better sense of the types of domains, regions in your protein that are...
I just found a platform that lets you run Calvados force field simulations without touching a terminal.It's called FastFold, and it has a built in app for Calvados molecular dynamics simulations.Here's how simple it is:Go to FastFold, click on Apps, and open Calvados.You can input your own sequence of interest, or start with the examples section. There are several proteins to choose from, and I would recommend starting with lysozyme.Click on it and you'll be prompted to a settings page for...
Throwback to 2014. I wanted to share with you a framework that helped me push forward when things got difficult.This is a photo of me in 2014, when I had just started a second internship at OSU while still an undergrad. I was new to the US, new to OSU, and well, new to everything. So of course I was intimidated. The framework I always played in my head is called BHP. Here’s how it works:1) B = Believe in what you do. It sounds super cliche, but if you truly love what you do, trust me, no...
I work with two very different groups of people who end up with the same question. Does this molecule actually work? Founders ask me this before an investor meeting, when a failed wet lab experiment could cost tens of thousands of dollars and months they do not have. PIs ask me this when they need simulation data for a manuscript but do not have the compute or the expertise in house to get it done. I am hosting a FREE Webinar where I will walk through exactly how I answer that question. I...
Sharing a few PyMOL lines I always use as a fast way to visualize binding pocket residues within 5Å of a ligand from MD simulation outputs!! These lines of code have always been a time saver for me. So hope they help you a lot in your research!! Here they are:remove solvent select binding_site, byres (resn LIG expand 5) hide everything show sticks, binding_site show spheres, resn LIG color purple, resn LIG zoom resn LIG, 5Let me know how it goes!! Best, Omar. © ProteinReach|2026...
I work with two very different groups of people who end up with the same question. Does this molecule actually work? Founders ask me this before an investor meeting, when a failed wet lab experiment could cost tens of thousands of dollars and months they do not have. PIs ask me this when they need simulation data for a manuscript but do not have the compute or the expertise in house to get it done. I am hosting a FREE Webinar where I will walk through exactly how I answer that question. I...
I’m always astonished when I see a paper using only docking to drive conclusions about the interactions of a protein-ligand complex. Please never rely exclusively on one ligand pose. Remember, proteins and ligands are dynamic structures that move, therefore the chances of docking reflecting a correct pose in the binding pocket of a protein are sometimes not the greatest! Hence, approaches like MD simulations can help increase your chances of success. How? Well .. MDS can help capture...
I spent years figuring out protein-ligand workflows the hard way. I put together this playbook to help you get ahead in protein modeling.When I started in protein modeling, I wanted to try everything at once: docking, MD, different force fields, etc, with no clear path or direction. That kind of abundant information doesn't help your learning. It actually slows you down. That experience is exactly why I put together this playbook.I put together a comprehensive framework to help you get...