Guided Intake
Upload receptor files, ZIPs, folders, or fetch structures by PDB ID when supported by the workflow.
Public docking-prep workflow
Build cleaner AutoDock Vina job packages from a guided browser workflow.
AutoDock-Vina PrepServer helps researchers collect receptor structures, define docking boxes, prepare proteins, upload ligand inputs, and export portable docking packages without hand-building every run directory.
What is AutoDock-Vina PrepServer?
AutoDock-Vina PrepServer is an AutoDock Vina web server and headless API for molecular docking preparation. It helps users organize receptor files, save docking-box coordinates, prepare receptor PDBQT assets, upload ligand inputs, and generate portable ZIP packages for downstream docking execution.
Docking Boxes
Use browser-guided structure viewing to define center coordinates and box size before packaging.
Portable Packages
Export ready-to-run ZIP archives for downstream AutoDock Vina execution in local or configured HPC environments.
What the server prepares
A practical bridge between structure files and downstream Vina runs.
The public site is designed for the preparation layer of molecular docking: organizing receptor inputs, storing docking box coordinates, converting receptor assets where supported, collecting ligand files, and generating a package that can be reviewed before execution.
It does not replace scientific judgment, parameter selection, receptor curation, or downstream validation. Instead, it helps make the setup steps visible and repeatable so researchers can spend less time rebuilding folders and more time inspecting the actual docking workflow.
For first-time users
Follow the browser workflow when you want visual checkpoints for receptor upload, docking center selection, ligand upload, and ZIP generation.
For teaching and onboarding
Use the staged interface to explain why docking preparation depends on file formats, box coordinates, receptor cleanup, and ligand provenance.
For scripted workflows
Use the headless API when a repeatable command-line or agent-driven docking package preparation flow is a better fit than the browser.
For public deployments
Treat public instances as public tools and avoid confidential structures or proprietary ligand libraries unless the deployment is governed for that use.
Connected ecosystem
Designed as a clean entry point into companion molecular design tools.
The PrepServer remains focused on docking package preparation while linking to related Schürer Lab and companion workflows for ligand exposure review, E3-recruiter exploration, induced-proximity design, and modeling support.
View the modules ecosystemQuestions, deployment feedback, or collaboration ideas?
Contact Joseph-Michael Schulz at jmschulz@med.miami.edu.
FAQ
AutoDock Vina PrepServer FAQ
Short answers for users deciding whether the web server, workflow guide, or API is the right entry point.
Is AutoDock-Vina PrepServer a docking results engine?
No. The site prepares and packages inputs for downstream AutoDock Vina execution. Docking runs, parameter choices, interpretation, and validation remain separate scientific steps.
What does the generated ZIP package contain?
The package is intended to collect prepared receptor assets, ligand inputs, docking center data, runner scripts, and instructions so the workflow can move into a local or configured compute environment.
Can I use the workflow without the browser?
Yes. The versioned headless API supports scripted workspace creation, receptor intake, center saving, receptor preparation, ligand upload, package building, artifact listing, and download.