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Projects / Programmes source: ARIS

Computer Algorithm Development for Macromolecular Simulations

Research activity

Code Science Field Subfield
1.07.00  Natural sciences and mathematics  Computer intensive methods and applications   

Code Science Field
P000  Natural sciences and mathematics   
Keywords
Molecular Modeling, Computer Simulations, Algorithms, Molecular Dynamics, Symplectic Methods, Normal Mode Analysis, Parallel Computational Methods, Parallel Molecular Visualization, Protein-Protein Binding Sites, Biologically Active Compounds
Evaluation (rules)
source: COBISS
Researchers (9)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  23422  PhD Urban Borštnik  Computer intensive methods and applications  Researcher  2008 - 2011  36 
2.  28560  PhD Nejc Carl  Computer intensive methods and applications  Junior researcher  2009 - 2011  23 
3.  02287  PhD Milan Hodošček  Chemistry  Researcher  2008 - 2011  281 
4.  06734  PhD Dušanka Janežič  Computer intensive methods and applications  Head  2008 - 2011  504 
5.  25435  PhD Janez Konc  Computer intensive methods and applications  Researcher  2008 - 2010  236 
6.  13627  PhD Franci Merzel  Computer intensive methods and applications  Researcher  2008 - 2011  218 
7.  19037  PhD Matej Praprotnik  Computer intensive methods and applications  Researcher  2008 - 2011  327 
8.  30286  PhD Blaž Vehar  Computer intensive methods and applications  Junior researcher  2009 - 2011  17 
9.  26516  PhD Jernej Zidar  Computer intensive methods and applications  Junior researcher  2008 - 2009  26 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,237 
Abstract
The goal of the proposed research is to introduce new improvements in computer simulation of macromolecules that increase the accuracy and efficiency of present-day computation approaches. We primarily aim to: improve algorithms for integration of classical and quantum equations of motion by further developing symplectic algorithms based on analytical treatment of high frequency motions; improve the treatment of the solvent in molecular dynamics simulation by developing explicit/implicit solvent methods in which the hydration water is represented explicitly while the surrounding bulk water is represented implicitly; and develop new algorithms for protein-protein binding site prediction. The proposed methodological improvements should significantly extend the scope of presently used algorithms in terms of length- and time-scales and thus contribute to the general applicability of computer simulation algorithms. The simulation results of selected examples will facilitate the understanding of some fundamental problems in molecular biology.
Significance for science
New developments in molecular dynamics integration methods can find wide applications in computer simulations of the structure and dynamics of biological macromolecules in contributing to higher precision and economy of computation. The new methods use less computer time and therefore extend the applicability of simulation strategies to larger systems and enable higher precision calculations. A particularly promising consequence of the enhanced possibilities offered by the new methods is the inclusion of solvent effects. This requires a major computational effort in present schemes, thus strongly limiting the number of solvent molecules that can be included in the simulation. The new methods should therefore highly improve on this important aspect of molecular simulations. From the practical point of view, protein engineering should benefit from the predicting capacity of the molecular dynamics simulation methods that would become more economical. Since protein engineering is a promising area of development in at least two institutes in Slovenia, the benefit of this research is obvious. The development of molecular dynamics algorithms as presented can be included as a software module in computer programs commonly used for molecular modeling of biological systems. The ability to improve the predicting power of methods used in the simulation of proteins is of paramount importance for protein engineering and is sealing the relation between the higher order structure of proteins and their biological function. The research carried out following this proposal is of great importance to the development of modern simulation techniques that hold the promise to greatly increase our ability to simulate large macromolecular systems with a reasonable amount of computational effort. It is expected that the product of this research effort will be added to the CHARMM (Chemistry at HARvard for Macromolecular Mechanics) program and distributed for use by others throughout the world.
Significance for the country
The purpose of the project is to develop, improve, and apply the computational methods for molecular dynamics simulations in the study of the structure and dynamics of biological macromolecules, such as proteins. The project focuses on specific problems of molecular biology, on code development and application, and also on its parallel implementation. An important component of the project involves close collaboration with the leading laboratories in this research field. The results of this research were published in international scientific journals and were presented at international scientific meetings. In collaboration between the Center for Molecular Modeling from the National Institute of Chemistry and Lek, a new Sandoz company, Drug Discovery we apply computer simulations to novel chemical entities (NCE's) in the antiinfective and cardiovascular therapeutic areas. We collaborate also with groups from the IJS, MF, FMF, BF, FF, FRI ( UL), and FAMNIT (UP). In collaboration with Lek, a new Sandoz company, Drug Discovery the Laboratory for Molecular Modeling is involved in several industrial projects that use molecular modeling methods for research into new drug leads. Industrial project for LEK, d.d., contract number BIO-6/2010: Computer modeling of biopharmaceutical molecules bt web server ProBiS. PI: Prof. Dr. Dušanka Janežič.
Most important scientific results Annual report 2008, 2009, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2008, 2009, final report, complete report on dLib.si
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