CompChem
From HP-SEE Wiki
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Our research is directed toward: | Our research is directed toward: | ||
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a) examination of the free-energy landscapes of highly potent and very selective antitumor agents, named CSAB (see Journal of Medicinal chemistry, 48, 5600-5603, (2005); The XVI European Symposium on Quantitative Structure-Activity Relationships and Molecular Modelling, 10-17 September 2006 Mediterranean Sea / Italy. Final program& General Information pp. 274-275; and The 18th European Symposium on Quantitative Structure-Activity Relationships, 19-24 September 2010, Rhodes, Greece. Final Program & Abstract Book, pp. 278-279), in explicit solvent clusters, having | a) examination of the free-energy landscapes of highly potent and very selective antitumor agents, named CSAB (see Journal of Medicinal chemistry, 48, 5600-5603, (2005); The XVI European Symposium on Quantitative Structure-Activity Relationships and Molecular Modelling, 10-17 September 2006 Mediterranean Sea / Italy. Final program& General Information pp. 274-275; and The 18th European Symposium on Quantitative Structure-Activity Relationships, 19-24 September 2010, Rhodes, Greece. Final Program & Abstract Book, pp. 278-279), in explicit solvent clusters, having | ||
different dielectric constants, H-bonding ability, and polarity, by medium lasting (~ 30ns) molecular dynamic simulations coupled with adaptive biasing force calculation; | different dielectric constants, H-bonding ability, and polarity, by medium lasting (~ 30ns) molecular dynamic simulations coupled with adaptive biasing force calculation; | ||
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b) Molecular dynamics simulations (~ 80 ns each) for “approach and entrance” of the group of compounds, which act as dual acetylcholine esterase (AChE) inhibitors, to enzyme active site. Whole systems (enzyme + inhibitor) for each compound are embedded in properly sized (large) solvent cluster. Last stage of each simulation includes adaptive biasing force calculation. | b) Molecular dynamics simulations (~ 80 ns each) for “approach and entrance” of the group of compounds, which act as dual acetylcholine esterase (AChE) inhibitors, to enzyme active site. Whole systems (enzyme + inhibitor) for each compound are embedded in properly sized (large) solvent cluster. Last stage of each simulation includes adaptive biasing force calculation. | ||
Revision as of 07:35, 6 July 2011
Contents |
General Information
- Application's name : Quantum Mechanical, Molecular Mechanics, and Molecular
Dynamics computation in chemistry
- Virtual Research Communities : Computational Chemistry Applications
- Scientific contact : Ivan Juranic, ijuranic@chem.bg.ac.rs
- Technical contact : Ivan Juranic, ijuranic@chem.bg.ac.rs
- Developers : Ivan Juranic, Univeristy of Belgrade, Faculty of Chemistry, Republic of Serbia
- Web site :
Application and Short Description
The project deals with modeling of molecular structure and mechanism of chemical reactions. Quantum mechanical, ab-initio, and DFT calculations will be applied for molecules that consist up to 250 atoms. Molecular mechanics and molecular dynamics simulation will be used for examination of ligands interaction with proteins and other biomacromolecules, as well as for conformational sampling of small molecules in explicit solvent cluster. In such simulations size of ligands should be up to 300 atoms; while biomacromolecule can have size of more than ten thousands of atoms. In the present stage, simulations were done by NAMD2.7.
Our research is directed toward:
a) examination of the free-energy landscapes of highly potent and very selective antitumor agents, named CSAB (see Journal of Medicinal chemistry, 48, 5600-5603, (2005); The XVI European Symposium on Quantitative Structure-Activity Relationships and Molecular Modelling, 10-17 September 2006 Mediterranean Sea / Italy. Final program& General Information pp. 274-275; and The 18th European Symposium on Quantitative Structure-Activity Relationships, 19-24 September 2010, Rhodes, Greece. Final Program & Abstract Book, pp. 278-279), in explicit solvent clusters, having different dielectric constants, H-bonding ability, and polarity, by medium lasting (~ 30ns) molecular dynamic simulations coupled with adaptive biasing force calculation;
b) Molecular dynamics simulations (~ 80 ns each) for “approach and entrance” of the group of compounds, which act as dual acetylcholine esterase (AChE) inhibitors, to enzyme active site. Whole systems (enzyme + inhibitor) for each compound are embedded in properly sized (large) solvent cluster. Last stage of each simulation includes adaptive biasing force calculation.
Several components of this approach require massive study of the vast parameter space and include tightly-coupled simulations with large memory requirements. Testing, benchmarking and production runs of some of the components can be done on standard Grid-type Linux clusters, but the core components require low-latency parallel environment. Postprocessing of trajectories, as well as output of (coupled) free-energy calculations, are also often memory demanding, so it is suitable to do such analysis on the nodes associated with the cluster where simulation were performed.
Problems Solved
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Scientific and Social Impact
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Collaborations and Beneficiaries
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Technical features and HP-SEE implementation
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Usage Example
- Primary programming language : Tobefilledin
- Parallel programming paradigm : Tobefilledin
- Main parallel code : Tobefilledin
- Pre/post processing code : Tobefilledin
- Application tools and libraries : Enumerate (comma separated)
- Number of cores required : Tobefilledin
- Minimum RAM/core required : Tobefilledin
- Storage space during a single run : Tobefilledin
- Long-term data storage : Tobefilledin
Publications and Presentations
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