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Research articles, tutorials, and practical guidance tagged MolNexus.
Find a method, workflow, scientific concept, or software decision.
Estimate Vina runtime from a representative local benchmark, then plan CPU allocation, exhaustiveness, concurrency, and batch throughput without relying on a universal minutes-per-ligand claim.
Read the analysisFilter the publication by research area or keyword.
Evidence-led articles on scientific methods, reproducible workflows, and software decisions.
Decide whether molecular dynamics should follow a Vina screen by the unresolved scientific question, decision value, model readiness, replicate plan, and evidence—not as a ritual confirmation step.
Choose between Vina and GNINA by the decision, target-relevant benchmark, deployment constraints, throughput, and reproducibility—not by assuming empirical or CNN scoring wins everywhere.
Build a kinase-specific Vina protocol around receptor state, the hinge and DFG motif, controlled preparation, pose review, and validation—without mistaking a hinge contact for proof of inhibition.
Audit a docking pose in five layers: molecular identity, pocket placement, physical plausibility, interaction recovery, and target-specific validation—without treating one Vina score as proof.
Use one reference control and one representative case to evaluate a molecular docking GUI, score workflow evidence, and make a defensible buy, defer, or reject decision.
Install AutoDock Vina 1.2.7 on Windows 11, verify the official EXE in PowerShell, fix path and config errors, and choose between CLI and a guided workflow.
Understand why PDBx/mmCIF is replacing legacy PDB as the complete archive format, what changes in 2027, how AlphaFold fits, and when conversion remains appropriate.
Prepare single ligands or SDF libraries for AutoDock Vina with Meeko while preserving chemical identity, state, atom mapping, validation decisions, and provenance.
Use molecular docking to test scaffold-hop candidates with explicit design constraints, controlled pose comparison, multi-evidence review, and prospective experimental closure.