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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.
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.
How to Evaluate a Molecular Docking GUI: A Two-Run Workflow Plan
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.
How to Run AutoDock Vina on Windows 11: Download, Verify, and Fix the “Flashing EXE”
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.