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I will perform molecular docking with autodock vina or quickvina gpu
Bioinformatics Engineer, Molecular Docking and Python Automation
Bioengineering researcher specializing in molecular docking, virtual screening, and bioinformatics automation. I help research labs turn slow manual workflows into fast, GPU-accelerated pipelines.
Ha...
About this Gig
Hi! I'm a bioengineering researcher with hands-on experience running large-scale molecular docking pipelines on GPU-accelerated Linux workstations.
WHAT YOU GET:
Professional docking with AutoDock Vina or QuickVina-GPU 2.1
Proper receptor & ligand preparation (PDBQT, protonation, charges)
Binding affinity scores with detailed analysis
Top binding poses ranked and visualized
Clean results in CSV/Excel + PDF report
WHY ME:
- GPU-accelerated workflow (10-100x faster than CPU)
- Real research experience: screened 180+ GB of ZINC database against bacterial drug targets
- Built automated pipelines for natural product virtual screening
- Custom Python scripts tailored to your workflow
WHAT TO SEND ME:
1. Your protein (PDB ID or PDB file)
2. Your ligands (SMILES, SDF, MOL2, or compound names)
3. Active site information (or I can detect it)
Need something custom or larger scale (5000+ ligands)? Message me before ordering and I'll build a custom package.
Looking forward to working with you!
Domain:
Machine Learning
•
Deep Learning
•
Generative Models
•
Other
Programming language:
Python
•
R
•
Colab
•
Other
Tools:
Jupyter Notebook
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TensorFlow
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Excel
•
Colab
•
Other
FAQ
Do I need to send the protein structure file?
Not necessarily. If you provide a PDB ID, I'll fetch and prepare the structure. If you only have a sequence, I can build a homology model or AlphaFold prediction (small additional cost via gig extras).
What docking software do you use?
Primarily AutoDock Vina and QuickVina-GPU 2.1 (GPU-accelerated). I can also use UniDock or PLANTS if your project requires them.
Can you handle larger virtual screening campaigns?
Yes. For larger libraries (500-50,000+ ligands), message me first and I'll build a custom package with appropriate pricing.
What files do I receive?
All output PDBQT files, log files, scoring tables (Excel/CSV), and a PDF report. Source files and Python scripts are included on Standard and Premium packages.
How do you ensure docking quality?
I validate setup with redocking of known ligands when crystal structures are available, use proper grid box definition, and apply standard preparation protocols (Gasteiger charges, polar hydrogens, flexible torsions).
