ChemServerOnline virtual screening for ligands and receptors
Structure based virtual screening without a cluster: paste a list of molecules, load one or more protein targets and ChemServer docks every pair, ranks the hits and writes the report.
Three kinds of screening
Ligand screening
Many molecules against one target. Rank a library of candidates, analogues or natural products by predicted binding to a single pocket and keep the best for the next step.
Receptor screening (inverse docking)
One molecule against many targets. Load a panel of PDB IDs to look for likely targets, check selectivity between related proteins or flag possible off target binding.
Matrix screening
Several ligands against several receptors in the same run. Each receptor keeps its own chain and target ligand, and the results come back as one ranked table per receptor.
How a screen runs
- Fetch targets by PDB ID (for example
1HSG, 3CLN, 5EHR) or upload PDB files. - Paste SMILES, one per line, or upload SDF, MOL2 and PDBQT files or a ZIP of PDBQT files.
- Choose the site: the co crystal ligand, the whole protein or your own grid.
- Pick an engine. AutoDock Vina for CPU runs; Vina-GPU or GNINA when speed or CNN rescoring matters.
- Start. Ligands are prepared, docked, scored and ranked while you do something else.
A typical CADD screening workflow
- Filter the library with RDKit descriptors: molecular weight, logP, TPSA and hydrogen bond counts for Lipinski's rule of five.
- Validate the setup by redocking the co crystal ligand (see the docking guide).
- Dock the filtered set with AutoDock Vina or Vina-GPU.
- Rescore the top hits with GNINA's CNN to reorder poses.
- Inspect poses and interactions with pose quality checks and the protein viewer.
- Confirm the most promising complexes with molecular dynamics (on request).
What you get back
- Ranked tables with the best score for every ligand receptor pair.
- Best and all poses for each pair, as PDBQT and PDB files.
- An Excel workbook to sort, filter and chart the hits.
- Full logs so every number can be traced.
Size of a screen
A free account screens up to 50 ligand receptor pairs per run, for example 50 ligands against one target or 10 ligands against 5 targets. Larger campaigns are possible on request: email chris@chemserver.online with the number of ligands and receptors.