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Research articles, tutorials, and practical guidance tagged MolNexus.
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Evidence-led articles on scientific methods, reproducible workflows, and software decisions.
Build a focused ligand library with traceable identities, chemical diversity, target-specific controls, verified compound availability, and a versioned docking manifest.
Learn how to curate existing-drug libraries, validate a molecular docking protocol, review structural hypotheses, and prioritize candidates for experimental repurposing studies.
Learn how molecular docking supports fragment growing, linking, and merging inside a practical Design–Make–Test workflow while preserving experimental evidence.
Use mk_prepare_receptor to create AutoDock Vina receptor PDBQT and box files while documenting parsers, residue decisions, outputs, validation, and provenance.
Learn what a PDBQT file stores, how ligand torsion trees differ from rigid receptor records, why bond orders can be lost, and what to inspect before an AutoDock Vina run.
Decide which waters, metals, ions, and cofactors belong in a docking receptor by biological role, structural evidence, ligand mechanism, force-field compatibility, and controlled validation.
Compare local, cloud, and hybrid molecular docking by real workload, data boundaries, runtime continuity, reproducibility, collaboration, governance, and total cost - not by deployment label alone.
A practical AutoDock Vina reporting checklist for preserving prepared inputs, software versions, search-box geometry, parameters, seeds, raw poses, failures, and the evidence needed to re-execute a docking study.
Choose a receptor by target state, local pocket evidence, ligand context, and validation. Compare when a holo, apo, AlphaFold, or receptor ensemble best fits a reproducible protein-small-molecule docking campaign.