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I will do molecular docking and MD simulations for drug discovery
Ali Hamza
About this gig
Are you looking to accelerate your drug discovery pipeline or gain deep structural insights into protein-ligand interactions?
I provide high-precision computational chemistry and molecular modeling services tailored for researchers, academics, and pharma startups. Utilizing validated workflows in structure-based (SBDD) and ligand-based (LBDD) drug design, I deliver reproducible, publication-ready results.
My Technical Services Include:
- Molecular Docking: Active site mapping and binding affinity evaluation using AutoDock Vina and Material Studio.
- Virtual Screening: High-throughput screening of massive ligand or small-molecule libraries.
- Quantum Chemical Optimization: Geometric optimization and electrostatic calculations using Gaussian.
- ADMET Prediction: In silico evaluation of pharmacokinetics and drug-likeness (Lipinskis Rule of 5).
- MD Simulations: Long-timeline dynamic tracking of structural stability, RMSD, RMSF, and hydrogen-bond analysis.
- Visualization: High-resolution 3D figures rendered via PyMOL.
What You Will Receive:
- All raw data files (.pdb,.pdbqt,.sdf,.mol2,and log/trajectory tracks).
- Ultra-high-resolution, publication-quality structural graphics.
- A comprehensive report
Get to know Ali Hamza
Ali Hamza
Molecular Docking ,Drug Discovery and Molecular Simulations Expert
- FromPakistan
- Member sinceJun 2026
Languages
English
Computational Chemist (SBDD), (LBDD), and molecular dynamics (MD) simulations.
I help researchers, pharma startups, and academics accelerate their drug discovery pipelines by providing high-precision in silico screening and structural analysis.
Core Expertise:
Molecular Docking: Protein-ligand, protein-protein, and virtual screening of massive compound libraries.
Molecular Dynamics (MD).
ADMET Prediction: In silico evaluation of pharmacokinetics, toxicity, and drug-likeness (Lipinski’s Rule of 5).
Tools:
Docking: AutoDock Vina ,Material Studio , Gaussian
Visualization & Analysis: PyMOL.
FAQ
What input files or data do you need from me to start the project?
For the target protein, I need the PDB ID or an optimized .pdb/.cif file. For the ligands, you can provide the chemical names, SMILES strings, PubChem CIDs, or structures in .sdf or .mol2 formats. If the binding site is known, please share the specific active site residues or grid box coordinates.
Which specialized software tools and computational frameworks do you use?
I utilize industry-standard tools for maximum reproducibility: AutoDock Vina and Material Studio for precise molecular docking and virtual screening; Gaussian for quantum chemical or DFT ligand optimizations; and PyMOL alongside Discovery Studio for high-resolution 3D visual analysis and interaction
Are the raw trajectory and analysis data files included in the delivery?
Yes. Along with a comprehensive written analysis report containing structural figures and data charts, I will provide all raw outputs—including docked poses (.pdbqt / .pdb), parameterized topologies, and simulation data tracks—so you can verify or continue the workflow locally.
Can you perform Molecular Dynamics (MD) simulations on large complexes or custom systems?
Yes, I can set up simulations for standard protein-ligand complexes. However, for membrane-bound proteins, massive protein-protein interfaces, or long timeline requests (>50 ns), please contact me first so we can properly estimate the structural parameterization needs and computational run
Will the structural graphics and data charts be suitable for research publications?
Absolutely. The 3D molecular visualization graphics generated via PyMOL are rendered in high-resolution, high-DPI quality suitable for peer-reviewed journal publications, thesis submissions, or academic grant proposals.
