MORDOR: Molecular Docking Optimizer
Overview
The Molecular Recognition with a Driven Dynamics Optimizer (MORDOR) is an advanced computational tool designed for flexible docking simulations. It leverages molecular dynamics to predict the interaction patterns between ligands and target macromolecules, optimizing binding poses and energy states with high precision.
Key Applications
- Flexible Ligand Docking: MORDOR supports the docking of ligands with flexible structures, accommodating various conformational changes that occur during the binding process.
- Dynamic Binding Simulations: Using driven dynamics, MORDOR simulates the transition states and interaction pathways that ligands undergo, providing insights into the molecular recognition mechanisms.
- Structure-Activity Relationship (SAR) Analysis: The tool integrates SAR analysis to correlate docking outcomes with biological activity, enhancing the understanding of how molecular structures influence function.
Features
- Driven Dynamics Optimization: Incorporates molecular dynamics-driven simulations to explore a wide range of conformations and docking sites, improving accuracy in predicting ligand binding affinities.
- Energy Minimization: Utilizes root-mean-square-deviation (RMSD)-driven energy minimization techniques to refine the docked poses, allowing for precise fitting into the binding pocket.
- Compatibility with Multiple Targets: MORDOR is designed to work with a variety of biological targets, including proteins, nucleic acids, and other macromolecules.
Research Applications
- HIV-1 RNA Maturation: MORDOR has been used to study the binding characteristics of small molecules that mimic nucleocapsid protein-induced maturation of stem-loop-1 of HIV-1 RNA, highlighting potential therapeutic targets.
- Telomerase RNA Ligand Discovery: Through flexible-target virtual screening and NMR integration, MORDOR assists in identifying new ligands targeting human telomerase RNA, a crucial component in cancer research.
- Antifungal Drug Binding Studies: Structural characterization of CYP51 from Trypanosoma species has been achieved using MORDOR, revealing how drugs such as posaconazole and fluconazole interact with their targets.
For further details, access the following resources:
If you encounter any issues or need additional support, please contact Christophe Guilbert at cguilbert@picasso.ucsf.edu.