Molecular modeling
Russian response
Olga Gushchina, Rosnauka
rus-img.com
Is it possible to simulate the structure and functions of molecules on a computer? And how can molecular processes be visualized?
Molecular modeling in biology and chemistry has long ceased to be something fantastic. Computer modeling methods are particularly widely used where obtaining experimental results is extremely difficult (even practically impossible) or too costly.
At its core, the methods of molecular modeling can be compared, perhaps, with the means of automatic design (CAD). The tasks here are often similar: as a new aircraft is designed in CAD, so a new compound can be "constructed" in molecular modeling. That's just the object of research here is more complicated, and the properties of the studied systems are not always so well known.
Molecular modeling is a kind of scientific tool, the target areas for which are pharmacology, biotechnology, materials science. At the same time, this tool itself is the source of a wide range of scientific tasks - from the development of new, more advanced models describing the properties of existing systems, to the creation of new software packages that implement the widest range of theoretical methods and approaches of molecular modeling.
Let's try to figure out what arsenal of software products for computer modeling of individual molecules and periodic structures is currently available to Russian and foreign scientists?
Foreign developmentsOne of the first software packages for molecular modeling – GAUSSIAN – was developed back in 1970 by Nobel laureate John Paul, and today it confidently remains among the "leaders", remaining one of the most widespread and at the same time one of the most functional complexes.
In the arsenal of the software package there are more than 80 calculation methods for determining the structure and energy, as well as various characteristics of molecules and compounds. However, this software product also has its drawbacks, which include high requirements for hardware, as well as relatively low speed of operation. In addition, the development is distributed exclusively on a commercial basis.
Another software product, or rather, the American version of the package – GAMESS (US) – is distributed on a free basis (subject to non-commercial use) and is currently supported by a group of developers from Iowa State University.
Among the features of the software package, first of all, the methods of computational quantum chemistry, and therefore, in terms of functionality, the product is inferior to many competitors: for example, the methods of molecular mechanics remained completely unrealized in the software.
In contrast to the above-mentioned development, the GROMACS and AMBER software packages, on the contrary, are "sharpened" to perform calculations in the field of molecular dynamics, i.e. they allow determining the trajectories of motion and characteristics of the interaction of molecules based on "simple" equations of classical Newton mechanics. This means that it is simply impossible to calculate the chemical reaction in such programs.
Of course, the entire list of foreign software for molecular modeling is not limited to this list, however, and the choice of a particular product depends on the specific scientific problem being solved.
nerohelp.info
Russian responseRussian scientists are also ready to offer their own solution to the problems of molecular modeling.
So, since the introduction of the GAMESS software package into the educational and research process of Lomonosov Moscow State University, Professor Alexander Granovsky has taken over its refinement and adaptation, as a result of whose efforts a new product has turned out - Firefly (formerly known as PC GAMESS).
Already in 1999, the package became completely software-independent of its "predecessor", and in 2008 it received a new name. It is noteworthy that about 95% of the source code was rewritten by the development team, thanks to which it was possible to significantly increase the speed of calculations performed, and the functionality of the software package expanded: in particular, new algorithms were developed, as well as existing algorithms for computational methods of quantum chemistry were improved.
Modern science does not stand still either: at the end of March this year, a new software package for molecular modeling – KVAZAR – was proposed by a group of scientists from Saratov State University (SSU).
sgu.ru
The project is managed by the Head of the Department of Radio Engineering and Electrodynamics, Head of the Mathematical Modeling Department of the Educational and Scientific Institute of Nanostructures and Biosystems (ONI NSiBS) SSU D.F.-M.N. O.E. Glukhova. The development is based on methods of molecular dynamics and quantum methods, classical approaches of molecular modeling, as well as original mathematical models created by the team of developers of the complex.
"Compared to well–known closed foreign software packages, our software package is characterized by an open architecture, which allows it to be adapted to solve any specific scientific problem," says Rosnauka.ru member of the scientific group of developers, leading programmer of the Mathematical Modeling Department of the NSiBS SSU, Candidate of Physical and Mathematical Sciences Anna Kolesnikova.
Scientists of the Moscow Institute of Physics and Technology (MIPT) have gone even further: in the near future, a distance learning course "Modeling of biological molecules on GPU" will start on the popular Internet resource Coursera, within which students will be invited to visualize processes in molecular systems using graphics processors, i.e., simply put, video cards available in computer.
From theory to practiceWhere can these software products be used in practice?
Molecular modeling methods are most widely used in biomedicine, materials science, as well as in the field of nanotechnology. The reason for this demand is simple: the use of computer models in most cases can significantly reduce the time and cost of developing a new material, nanodevice or drug. And if earlier the synthesis of hundreds and thousands of compounds, as well as their testing in cellular systems was carried out in practice, now these functions will be performed by software: it will be able to "predict", for example, how effective the synthesized compounds will be in the fight against viruses. At the same time, modeling the processes of deformation, formation and destruction of chemical bonds will allow calculating the strength of new composites even before they are put into mass production.
Portal "Eternal youth" http://vechnayamolodost.ru
15.07.2015