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MOLS 2.0: software package for peptide modeling and protein-ligand docking
1Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, India.
Journal of Molecular Modeling
|September 18, 2016
Summary
We enhanced MOLS software for protein and peptide conformational searches and molecular docking. MOLS 2.0 offers a new GUI and flexible receptor docking, improving accessibility for researchers.
Area of Science:
- Computational Biology
- Structural Biology
- Drug Discovery
Background:
- Previous versions of the algorithm, MOLS 1.0 and MOLSDOCK, enabled conformational searches and rigid receptor docking.
- These tools utilized mutually orthogonal Latin squares (MOLS) for conformational space sampling and mean field theory for analysis.
- Extensive validation supported the conformational search and rigid receptor docking functionalities.
Purpose of the Study:
- To enhance the MOLS algorithm by incorporating induced fit side-chain receptor flexibility for peptide ligand docking.
- To develop MOLS 2.0, a user-friendly version with a Java-based graphical user interface (GUI).
- To improve accessibility of peptide conformational search and docking algorithms to the research community.
Main Methods:
- Incorporation of induced fit side-chain receptor flexibility for enhanced docking capabilities.
- Development of MOLS 2.0 with a new Java-based graphical user interface (GUI).
- Benchmarking and extensive testing of the flexible receptor docking component.
Main Results:
- The flexible receptor docking component is currently undergoing rigorous benchmarking and testing.
- MOLS 2.0 provides a more accessible platform for both peptide conformational search and molecular docking.
- The software is freely available to the scientific community under a GNU Lesser General Public License.
Conclusions:
- MOLS 2.0 represents a significant advancement in computational tools for molecular modeling.
- The enhanced flexibility and user interface of MOLS 2.0 will facilitate broader adoption and application in research.
- Free distribution of MOLS 2.0 promotes collaborative research and accelerates discoveries in structural biology and drug discovery.
Keywords:
Graphical user interfaceInduced-fit dockingMolecular dockingMutually orthogonal Latin squares samplingProtein–ligand dockingMore Related Videos
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