About TLigBind
A virtual screening platform from the Trinh Lab at the University of Virginia. Run molecular docking experiments entirely from your browser — no command line or local installation required.
A typical screening run moves through these pages, in order:
Converts a molecule into a docking-ready PDBQT file.
How to use:
- Choose input type: Enter SMILES or Upload SDF
- Provide your molecule and give it a name
- Click Run Pipeline
What it does:
- Generates 3D coordinates from the molecular structure
- Adds hydrogens and optimizes geometry (MMFF94 force field)
- Assigns Gasteiger charges and AutoDock atom types (Meeko)
Output: Interactive 3D viewer + downloadable .pdbqt file ready for docking.
Converts a protein structure (PDB) into a clean, typed PDBQT for docking.
Input options:
- Upload a PDB or mmCIF file (.pdb / .ent; both legacy PDB and mmCIF formats supported)
- Enter a PDB accession code (fetched from RCSB, PDBe, or PDBj)
- Enter a UniProt ID (fetched from AlphaFold DB or SWISS-MODEL)
- Enter a ModelArchive model ID
- Fold a raw amino-acid sequence into a structure (ESMFold)
What it does:
- Displays structure in 3D — select which chain(s) to keep
- Rebuilds missing residues and atoms (PDBFixer)
- Assigns protonation states with PROPKA (pKa-aware; sets Asp/Glu/His/Cys/Lys/Tyr states and is metal-coordination aware)
- Energy-minimizes the structure (OpenMM, AMBER14 force field)
- Assigns Gasteiger charges and AutoDock atom types (Meeko)
The pipeline also extracts any native ligand and lets you define the Vina search box by native ligand, custom residues, whole molecule, or automatic pocket detection (Pocketeer).
Output: Downloadable .pdbqt receptor file + 3D viewer at each stage.
Submit a screening job with your prepared receptor and ligands.
- Upload individual .pdbqt files (up to 10)
- Upload a .zip archive of PDBQT files (up to 1 MB)
- Select a preset collection (FDA-Approved Drugs, SWEETLEAD)
- Upload your own .pdbqt receptor file
- Select from the community receptor library (includes recommended docking box)
- Use defaults (center at origin, 20×20×20 Å box)
- Upload a Vina-format config file
- Enter coordinates manually
- Use the community receptor's recommended box (if selected)
Click Submit Docking Job. You'll be redirected to My Jobs where you can track progress.
Monitor submitted jobs and download results.
Job statuses: Pending → Running → Done (or Failed / Cancelled)
What you can do:
- Watch progress in real time (X/Y ligands complete)
- Cancel running jobs (stops after current ligand)
- Delete old jobs
- Download results from completed jobs:
- CSV — binding affinities ranked strongest to weakest
- PDBQT poses — docked conformations for each ligand
- Vina logs — full scoring output
Jobs are retained for 7 days after completion.
Explore docked poses interactively without leaving the browser.
How to use:
- Upload a receptor structure
- Upload one or more docked-ligand pose files (Vina *_out.pdbqt)
- Step through the poses one at a time
What you get:
- Per-pose binding affinity and RMSD
- A ranked pose summary table and bar chart
- An interactive 3D view of the binding site
Share prepared receptors with the research community.
How it works:
- Prepare your receptor (using Receptor Prep or external tools)
- Go to the Contribute page and upload the .pdbqt file
- Fill in metadata: receptor name, Protein ID, organism, source database, description
- Optionally include a recommended docking box configuration
- Submit — an admin reviews your contribution
Once approved, your receptor appears in the community library on the Run Docking page. Other users can select it from a searchable dropdown and use your recommended docking box.
Understanding Your Results
Ranked table of ligands with binding affinity in kcal/mol. More negative = stronger binding. Hits below -7 kcal/mol are generally considered promising leads.
Predicted binding conformations. Open in PyMOL or UCSF Chimera alongside your receptor to visualize how the ligand sits in the pocket.
Full AutoDock Vina output per ligand — all binding modes, affinities, and RMSD between poses. Useful for assessing docking quality.
PDBQT File Requirements
If you prepare files with external tools (not TLigBind's built-in prep), they must meet these requirements:
- .pdbqt format (not .pdb or .mol2)
- Single molecule per file (one ROOT...TORSDOF block)
- Valid AutoDock atom types (A, C, N, NA, OA, HD, F, Cl)
- Must end with a TORSDOF line
- .pdbqt format
- Single rigid structure (no MODEL tags)
- Flexible residues not supported
- Compatible with AutoDock Vina 1.2.5
Docking Box Parameters
The search space tells Vina where on the protein to look for binding.
| Parameter | Description | Default | Units |
|---|---|---|---|
| center_x/y/z | Center of the search box | 0.0 | Angstroms |
| size_x/y/z | Dimensions of the search box | 20.0 | Angstroms |
| num_modes | Number of binding poses per ligand | 9 | — |
| energy_range | Max energy difference from best pose | 3.0 | kcal/mol |
- Known binding site: Open your receptor in PyMOL or Chimera, center the view on the active site, and read off the xyz coordinates. A 20-30 Angstrom box covers most pockets.
- Unknown site: Use a larger box (30-40 Angstroms) centered on the protein's geometric center. Slower but searches the whole surface.
- Default (0, 0, 0): Only correct if your PDB is centered at the origin. Most are not — always verify.
Troubleshooting
Ligand failed to dock
- Not a valid PDBQT — Must contain ATOM/HETATM records with AutoDock atom types. A renamed .pdb won't work. Use Ligand Prep to convert.
- Missing TORSDOF line — Required by Vina at the end of each ligand file.
- Incompatible atom types — Files from older AutoDock tools may have types Vina doesn't recognize. Re-prepare with Ligand Prep.
- Multi-model file — Only the first molecule is docked. Use one file per ligand.
Ligand Prep pipeline failed
- Invalid SMILES — Check for typos. Verify with PubChem Sketcher.
- SDF won't parse — Must contain a single molecule with valid coordinates. Multi-molecule SDFs are not supported.
- 3D embedding failed — Very large or highly strained molecules may fail. Try a different conformer approach externally.
Receptor Prep pipeline failed
- Invalid PDB — Must contain at least one protein chain. Ligand-only or water-only files will fail.
- AlphaFold fetch failed — Verify the UniProt ID is correct. Not all proteins are in AlphaFold DB.
- Energy minimization diverged — Rare. Can happen with badly clashing atoms. Try a different PDB source.
- Chain break / template error — Set Missing residues to rebuild_all, or set Energy minimization Max steps to 0, then rerun.
Job is stuck or very slow
- Large library — Each ligand takes 10-60 seconds. A 100-ligand library may take 30-90 minutes.
- Large search box — Bigger boxes mean more computation. Keep to 20-30 Angstroms for known sites.
- 30-minute timeout — If a single ligand exceeds 30 minutes, it's skipped and marked as failed.
Can't find my results
- Go to My Jobs — all submitted jobs are listed with their status.
- Completed jobs have download buttons for CSV, poses, and logs.
- Jobs are automatically removed after 7 days.
About the Trinh Lab
TLigBind is developed by the Trinh Laboratory in the Department of Pathology at the University of Virginia School of Medicine.
The Trinh Lab uses computational and experimental approaches to investigate how proteins and noncoding RNAs regulate gene expression through chromatin structure in myeloid cell development, innate immune function, and disease. A major focus is identifying actionable molecular targets and developing therapeutic strategies for cancer (including acute myeloid leukemia) and neurodegenerative disorders.
TLigBind grew out of the lab's collaborative virtual screening efforts — supported by a UVA Cancer Center pilot grant and the DAC Analytics Resource Award — to make structure-based drug discovery accessible to researchers without computational chemistry expertise.
Principal Investigator: Bon Q. Trinh, Ph.D.
TLigBind development team: Abraham Tedla, Patrick Maloon, Pranav Sridhar, Varun Bhatnagar (UVA School of Data Science Capstone, 2025–2026)
Links: