Structural Biology

From structure to scored pose — molecular docking with Vina and GNINA, pocket detection, interaction analysis and the repair steps in between.

7 toolsVina + GNINAPocket · Interaction · Repair
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Rainbow ribbon diagram of a protein structure
Molecular Docking
7 tools

From structure to scored pose

Check the structure, find the pocket, dock the ligand and read the contacts that actually drive binding.

Rainbow ribbon diagram of a protein structure

Molecular Docking

ESMFold receptor, druggable pocket detection, then AutoDock Vina with a GNINA re-score.

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Protein surface with a gold ligand bound in the pocket

Protein–Ligand Docking

Prepare the receptor, dock the ligand and rank poses by Vina–GNINA agreement.

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Protein binding pocket with a ligand inside a mesh volume

Binding Site Detection

Detect druggable pockets, rank them by druggability and place the docking box.

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Ramachandran plot of a protein backbone showing allowed and disallowed regions

Structure Quality Analyzer

pLDDT confidence, steric clashes, Ramachandran outliers and missing residues — before you dock.

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Glutamate-gated chloride channel in complex with the ligand ivermectin

Interaction Analyzer

Hydrogen bonds, hydrophobic contacts, salt bridges and π-stacking, resolved per residue.

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Markov state model of protein folding pathways from the unfolded to the native state

Structure Regeneration

Model missing loops, resolve clashes and refine low-confidence regions before docking.

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Space-filling model of a DNA double helix

DNA 3D Viewer

Rotate a double-helix model — ball-and-stick to cartoon, colored by base or strand.

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Open any tool above directly — no installation, no desktop software. Browse all hubs or see what each plan unlocks.

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