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I will perform docking, virtual screening and MD simulations
Molecular Biologist, MD Simulations and Molecular Docking Expert
I am a Molecular Biologist specializing in structural bioinformatics and Computer-Aided Drug Design (CADD). I provide comprehensive in silico analysis services for researchers, academic studies, and b...
About this Gig
I provide in silico structural analysis and computational molecular modeling using standard bioinformatics pipelines.
Target protein preparation and binding pocket validation
Pharmacophore-based Virtual Screening
Molecular Docking (Protein-Ligand / Protein-Protein interactions)
Molecular Dynamics (MD) Simulations (50ns - 100ns+)
Trajectory Analysis (RMSD, RMSF, Rg, SASA, Hydrogen bonds)
Binding Free Energy Calculations (MM/PBSA)
I provide all raw trajectory data, processed CSV files, and exact parameter files (.mdp, .conf) used during the simulations. All analyses are conducted using fully documented, reproducible pipelines so you can easily validate and replicate the results for your publications.
Need a custom workflow for your project? Every biological target has different requirements so please send me a message with your specific project details before placing an order so we can discuss the exact technical parameters and delivery timelines for your research.
FAQ
What information do I need to provide to start the project?
You need to provide the target protein's PDB code or crystal structure file (.pdb). For ligands, please provide chemical structures in SMILES, SDF, or PDB format.
What if my target protein does not have an experimental crystal structure?
I can perform homology modeling (using Swiss-Model or similar tools) to predict the 3D structure of your protein before proceeding with docking or MD simulations.
Do you provide the raw trajectory files?
Yes. Since MD trajectory files (.xtc, .trr) are often very large (GBs), I will provide them via a secure cloud storage link. All parameter files (.mdp) and topology files (.top, .itp) will also be included for full reproducibility.
Can you perform calculations for non-standard residues or metal ions?
Yes. I can handle non-standard residues and metal-containing active sites (Holo-forms) by generating specific topologies and conducting DFT-based optimizations via ORCA where necessary.
Are the plots and renders provided in publication-ready quality?
Yes. I provide high-resolution (300-600 DPI) PyMOL renders and publication-quality plots (via Matplotlib/Seaborn). All visualizations are formatted to meet the standards of major scientific journals.
Can you handle long-term simulations beyond 200ns?
Yes, I can handle microsecond-scale simulations. However, since these require significant computational resources and time, please message me first for a custom offer so we can plan the timeline and resource allocation accordingly.
