Post by Omar Soliman

This is not just another computational workflow. For more than four months, three repositories have been sitting in the back of my mind — not only as coding projects, but as an accumulation of experience from tackling many repeated problems in computational drug discovery. Preparing structures. Defining uncertain binding sites. Running docking across tools. Interpreting ligand–protein interactions. Analyzing molecular dynamics outputs. Trying to connect structural results back to biological meaning. At some point, I realized that the real challenge was not only running each step. It was keeping the whole reasoning process connected. I wrote a LinkedIn article about this experience and about three repositories I have been developing: ApoSight — for moving from apo or predicted protein structures toward docking-ready binding-site definitions. OmniDock — for organizing multi-engine docking, post-docking analysis, interaction mapping, and ranking. ClarityDynamics — for converting GROMACS molecular dynamics outputs into clearer structural and quality-control evidence. For me, these repositories are not only code. They are a way of giving back part of the accumulated information, friction, debugging, and experience that came from trying to hold this kind of computational work together. The larger direction I am interested in is not a linear pipeline, but an iterative loop: structure, docking, dynamics, omics, single-cell biology, perturbation reasoning, and back again to better target and ligand prioritization. A ligand should not only “dock well.” It should make sense structurally, dynamically, biologically, and contextually. #ComputationalDrugDiscovery #Bioinformatics #MolecularDocking #MolecularDynamics #GROMACS #AlphaFold #SingleCell #MultiOmics #SystemsBiology #DrugDiscovery #OpenScience