Overview of key molecular simulation methods (QM, MD, CGMD, MC, BD, LD, DPD) and their strategic applications in drug discovery pipelines.
Build one graph of drugs, proteins, pathways, and a disease, embed it, and rank candidates by proximity to the disease node. Three ways of reading that ranking, then an assay.
Practical guide to checking AlphaFold-predicted protein models using pLDDT, PAE, geometry validation tools, structural comparisons, and functional tests.
A random forest on the B3DB blood-brain barrier set, scored on a held-out split, then opened with impurity importance and SHAP. TopoPSA is in the descriptor block only if you select that block on purpose.
A paper is an argument with a paper trail. The reader should be able to find the question, the evidence, and the limit of that evidence without opening your notebooks.
A 3D-QSAR model maps aligned molecular fields onto potency. The statistics say whether it predicts. The contours say where a chemist might change the molecule. Both depend on the alignment.
Long reads span a microbial genome and short reads correct it. This note is the hybrid path from quality control through Flye, two polishing steps, and BUSCO, QUAST, Prokka, and RAST.
A chemical table becomes a decision only after the row is defined, the model is scored on rows it did not fit, and the next experiment is allowed to disagree.
Turn a SMILES table into PaDEL fingerprints and a random forest, then score a held-out split with Matthews correlation. The cross-validation number is computed, not assumed.
What one molecular dynamics step does: take the forces on the current configuration, move the atoms by a few femtoseconds, and accumulate a trajectory.
