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BioChemIntelli Insights
Find candidate docking sites without a reference ligand using biological evidence, P2Rank, and fpocket, then document uncertainty before choosing a box.
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Latest publications
Evidence-led articles on scientific methods, reproducible workflows, and software decisions.
Evaluate a Virtual Screen: EF1% and Precision–Recall from a Ranking Table
A favorable docking score does not tell you whether a ranked list retrieves known actives early. Follow a complete numerical example and distinguish early enrichment from whole-ranking metrics.
Redocking vs Cross-Docking: Test a Protocol Across Receptor Conformations
A successful redocking pose does not establish transfer to another receptor conformation. Four small Vina runs show why seeds, coordinate frames and failed controls belong in the report.
Ligand Protonation and Tautomers for AutoDock Vina: How to Choose and Track Chemical States
Choose and track ligand protonation and tautomer states before AutoDock Vina. Use an assay-aware policy, stable state IDs, and fair compound ranking.
How to Calculate Redocking RMSD for AutoDock Vina: Atom Mapping, Symmetry, and Common Errors
Calculate redocking RMSD in the receptor frame, check atom mapping and symmetry, and avoid misleading ligand alignment with a tested RDKit example.
How Long Does AutoDock Vina Take? A Benchmark-First Guide to CPU Cores, Exhaustiveness, and Batch Size
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.
Molecular Docking vs Molecular Dynamics: When Should MD Follow an AutoDock Vina Screen?
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.
AutoDock Vina vs GNINA in 2026: When Empirical Scoring or CNN Rescoring Fits Better
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.
How to Dock Kinase Inhibitors with AutoDock Vina: Receptor State, Hinge Contacts, DFG Motifs, and Controls
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.
How to Check a Molecular Docking Pose Beyond the Vina Score: PoseBusters, PLIFs, and Interaction Recovery
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.