I will perform docking and advanced molecular dynamics simulation

Are you looking for expert-level Molecular Dynamics (MD) Simulation and Molecular Docking services for your research project, publication, or drug discovery work? You are in the right place!

With deep expertise in computational biology and chemistry, I offer comprehensive MD simulations and advanced analysis using industry-standard tools like GROMACS, AMBER, BIO3D, and others.

Services I Offer:

Molecular Docking:

•    Protein-ligand docking
•    Docking score analysis
•    Binding pose visualization

Molecular Dynamics Simulation (MDS): (Protein-Ligand, Protein-Protein, Protein-DNA/RNA)

•    Full MD pipeline
•    Up to 2000 ns or more simulations using GROMACS

Post-MD Analysis:

•    RMSD
•    RMSF
•    Rg
•    SASA & Buried SASA 
•    Hydrogen bond
•    Protein Ligand distance 
•    Secondary Structure Analysis
•    Principal Component Analysis (with Bio3D) 
•    FEL (Free Energy Landscape) 
•    DCCM 
•    Porcupine plots
•    3D correlated & anti-correlated motion networks
•    MMGBSA and MMPBSA
• Per-residue decomposition energy analysis
• MDS video

Tools & Software Used:

GROMACS | AMBER | BIO3D | VMD | PyMOL | UCSF Chimera | AutoDock | MMGBSA/MMPBSA | MDAnalysis | Schrödinger |PyRx |BIOVIA Discovery Studio|XMGrace