Question 1

What is molecular docking?

Accepted Answer

Molecular docking predicts how a small molecule binds to a protein target and estimates the binding affinity (in kcal/mol). Liganx runs docking online in your browser using GPU-accelerated AutoDock Vina (QuickVina2) and the Boltz-2 machine-learning model, with no software to install.

Question 2

Is Liganx molecular docking free?

Accepted Answer

Yes. Liganx gives you free online molecular docking runs with no install and no credit card. You dock wild-type and mutant targets, view 3D poses, and export results. Paid tiers add bulk virtual screening of hundreds of compounds.

Question 3

Do I need to install any software?

Accepted Answer

No, Liganx is fully web-based. Pick a protein target (curated catalog, RCSB PDB search, or your own upload) and compounds (sketch, paste SMILES, or upload a CSV/SDF), and everything runs on cloud GPUs. Nothing to download or configure.

Question 4

Which docking engine does Liganx use?

Accepted Answer

Liganx docks with AutoDock Vina (QuickVina2-GPU), re-scores with Vinardo for sharper close-analog ranking, and also supports the Boltz-2 co-folding model. Every pose is checked with PoseBusters physics validation so you can trust the geometry.

Question 5

What is mutation-aware docking?

Accepted Answer

Mutation-aware docking compares how a compound binds the wild-type protein versus clinically relevant mutants, such as EGFR T790M, BCR-ABL T315I, BRAF V600E, or KRAS G12C, in a single run, so you can see which compounds keep or gain selectivity against drug-resistance mutations.

Question 6

What do I need to run a docking?

Accepted Answer

A protein structure (a 4-character PDB ID like 4OBE, an RCSB search, or an uploaded PDB) and one or more compounds as SMILES, a 2D sketch, or an uploaded file. Liganx handles receptor preparation, mutation building, docking, and pose scoring automatically.