01
Workspace creation
A workspace isolates receptor files, center tables, ligand uploads, logs, and generated package artifacts.
Job root
Workflow guide
From receptor intake to a downloadable docking package.
AutoDock-Vina PrepServer turns a messy docking setup into a staged, traceable pipeline: receptor intake, docking box definition, receptor preparation, ligand intake, package generation, and downstream execution.
How the docking-preparation workflow works
The workflow moves from workspace creation to receptor intake, docking-box coordinate selection, receptor PDBQT preparation, ligand upload, package generation, and downstream AutoDock Vina execution. Each stage creates state that can be inspected before building the final ZIP package.
Pipeline map
The thread connects every preparation decision.
Each stage produces a state the next stage depends on. Receptors need centers, centers need prepared receptor outputs, packages need ligands, and downstream docking needs the final ZIP plus a working Vina executable.
02
Receptor intake
Upload receptor files or fetch structures by PDB ID. The server normalizes receptor storage under the workspace.
PDB / CIF / PDBQT
03
Docking box selection
Save an XYZ center and box size for each receptor so the generated Vina configuration has a defined search space.
vina_centers.csv
04
Receptor preparation
Clean the receptor, apply selected cleanup options, and convert receptor structures into docking-ready PDBQT files.
Open Babel
05
Ligand intake
Upload SDF, SMI, SMILES, CSV, ZIP, or folder-style ligand inputs. CSV workflows can preserve ligand provenance.
SDF / SMI / CSV
06
Package generation
Build a portable ZIP or optional LSF package containing receptors, ligands, centers, runner scripts, and instructions.
job.zip
Stateful by design
Failures become visible before docking starts.
Instead of discovering a broken setup after hours of compute time, each preparation checkpoint can be inspected: receptor state, saved centers, PDBQT conversion, ligand upload status, package artifacts, and final ZIP download.
Receptor registered
Receptors/3eky.pdb
Center saved
3eky.pdbqt → [x, y, z]
Receptor prepared
converted_count: 1
Ligand uploaded
accepted_count: 1
Package ready
job.zip
Browser workflow
Use the visual workflow when you want a guided, human-readable setup. This is ideal for first-time users, classroom demonstrations, or debugging receptor and ligand preparation interactively.
Open browser workflowHeadless API workflow
Use the API when you want scripted, reproducible docking package creation. Every browser stage has a corresponding endpoint under the versioned API.
Open API documentationReceptor intake
Start a workspace, then upload a single receptor, upload a ZIP or browser-selected folder of receptors, or fetch by PDB ID where supported.
Docking box selection
Open receptors in the viewer and save a docking center by supported methods such as ligand/residue selection, pasted XYZ coordinates, or clicked atoms in the structure view.
Receptor preparation
Review cleanup options such as HETATM or chain removal, choose preparation settings, and generate receptor files suitable for downstream docking package assembly.
Ligand intake
Upload ligand inputs as SDF, SMILES, SMI, CSV, ZIP, or browser folder inputs where supported. CSV inputs require selecting the SMILES column before building.
Package generation
Build a portable ZIP for generic local use, or choose the optional LSF/HPC-oriented package mode when the deployment enables that workflow.
Running generated packages
Move the ZIP to the execution environment, unpack it, activate the docking environment, and follow the package README or included runner scripts. The web app prepares the package; docking execution happens downstream.
Safety and data note
Public deployments should not receive confidential structures or ligand libraries unless the instance is configured, governed, and operated for that use.
Ready to build a docking package?
Start with the guided browser workflow, or use the API page when you want a fully scripted setup.
FAQ
Workflow questions
Which workflow stage should I check first when a package will not build?
Check whether the workspace exists, each receptor has a saved docking center, receptor preparation completed, and ligand input was uploaded with any required CSV SMILES column selection.
Does saving a docking box guarantee the correct biological binding site?
No. The saved center and size define the search space for packaging, but selecting a biologically appropriate site requires domain knowledge and downstream review.
When should I use the API instead of the browser workflow?
Use the browser when you need visual inspection and teaching-friendly checkpoints. Use the API when you need repeatable scripted package preparation, automation, or integration with another workflow.