Adenylate kinase 1,656 heavy atoms moving between the open (PDB 4AKE) and closed (PDB 1AKE) states, from a real transition trajectory.
Service 01
Molecular docking and virtual screening
We dock your ligands into your target, screen compound libraries, and show exactly how each molecule binds: scores, poses and the residues that hold it. Results for one target in about 2 days.
What we do
The work, step by step
- 01
Target and ligand preparation
Your protein from the PDB or a predicted model, cleaned and protonated; ligands built, minimised and converted to the right formats.
- 02
Binding-site definition
From a co-crystallised ligand, the literature or a pocket search, agreed with you before docking starts.
- 03
Docking and virtual screening
Single ligands or whole libraries of phytochemicals, drugs or designed compounds, ranked by binding score.
- 04
Interaction analysis
Hydrogen bonds, hydrophobic contacts, salt bridges and π-interactions for the top poses, as 2D and 3D diagrams.
- 05
ADMET and toxicity
Pharmacokinetic and toxicity prediction for the best hits, so you can see which ones are worth taking further.
- 06
Stability check by molecular dynamics
Optional: the best complexes simulated for 100 ns or more to test whether the pose holds.
You receive
- Docked complexes as PDB files
- A ranked table of binding scores
- 2D and 3D interaction diagrams for the top poses
- ADMET and toxicity tables
- A written methods and results section
Typical turnaround
2 days for one target
Counted from the day we receive your files. Larger studies get their own timeline with the quote. All turnaround times
Tools
AutoDock Vina, PyRx, Discovery Studio and ADMET prediction tools; GROMACS for follow-up dynamics.
Who works on it
Muhammad Zohaib · Dr. Fariha Javaid, with the BioInfoX research team. We take full responsibility for every analysis we perform.
Start
Send us your system and your question.
Structures, sequences or data, your research question and your deadline. We reply with the scope, the timeline and a quote.