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I will perform molecular docking and MD simulation
Bioinformatics Computational Biology Specialist
Need reliable bioinformatics or computational analysis for your research?
I am an MS Bioinformatics researcher at NUST, working in genomics, computational drug discovery, and biomedical AI. My servic...
About this Gig
Looking for reliable molecular docking and molecular dynamics simulation for your drug discovery research?
I provide end-to-end computational drug discovery analysis, from protein and ligand preparation to molecular docking, protein-ligand interaction analysis and GROMACS molecular dynamics simulation.
MY SERVICES INCLUDE
- Protein and ligand preparation
- Protein-ligand molecular docking
- Molecular docking using AutoDock Vina and related tools
- Binding affinity and docking score analysis
- Docking pose evaluation
- 2D and 3D protein-ligand interaction analysis
- Binding-site and interacting-residue analysis
- Virtual screening of compound libraries
- Comparative ligand ranking
- Drug-likeness analysis
- ADMET and toxicity prediction
- Molecular dynamics simulation using GROMACS
- RMSD analysis
- RMSF analysis
- Radius of gyration (Rg)
- SASA analysis
- Hydrogen-bond analysis
- PCA and trajectory analysis when required
- MM-PBSA binding free-energy analysis when applicable
- Publication-quality figures and result tables
TOOLS
GROMACS | AutoDock Vina | PyMOL | Chimera/ChimeraX | Discovery Studio | SwissADME | Python | related computational drug-discover
Service type:
Research
Language:
English
Delivery style preference
Please inform the freelancer of any preferences or concerns regarding the use of AI tools in the completion and/or delivery of your order.
Academic work to be done for you, is unethical since it violates most schools’ Honor Codes.
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FAQ
What information do you need to start molecular docking?
Please provide the target protein structure or PDB ID, ligand structures or compound names/IDs, your research objective and the expected binding site if known. If the binding site is not known, mention this before ordering so the appropriate workflow can be discussed.
Which software do you use for molecular docking?
Depending on the project, I can use AutoDock Vina and associated protein and ligand preparation tools. PyMOL, Chimera/ChimeraX, Discovery Studio and related software can be used for molecular visualization and interaction analysis.
Do you perform molecular dynamics simulations?
Yes. I perform GROMACS-based molecular dynamics simulations with analyses such as RMSD, RMSF, radius of gyration, SASA and hydrogen bonds. Additional trajectory analyses can be included depending on the research objective.
Can you perform 50 ns or 100 ns MD simulations?
Yes. MD simulations can be performed for different durations depending on the molecular system and study objective. Please contact me before ordering longer simulations such as 100 ns or above so the computational requirements can be evaluated
Do you perform MM-PBSA binding free-energy analysis?
Yes. MM-PBSA or related binding free-energy analysis can be included where appropriate for the molecular system and simulation workflow.
Can you perform virtual screening?
Yes. I can perform virtual screening against a target protein. Large compound libraries should be discussed before ordering because pricing and delivery depend on the number of compounds, targets and downstream analyses required.
