Computational methods for small molecules
نویسندگان
چکیده
Metabolism is the system of chemical reactions sustaining life in the cells of living organisms. It is responsible for cellular processes that break down nutrients for energy and produce building blocks for necessary molecules. The study of metabolism is vital to many disciplines in medicine and pharmacy. Chemical reactions operate on small molecules called metabolites, which form the core of metabolism. In this thesis we propose efficient computational methods for small molecules in metabolic applications. In this thesis we discuss four distinctive studies covering two major themes: the atom-level description of biochemical reactions, and analysis of tandem mass spectrometric measurements of metabolites. In the first part we study atom-level descriptions of organic reactions. We begin by proposing an optimal algorithm for determining the atom-to-atom correspondences between the reactant and product metabolites of organic reactions. In addition, we introduce a graph edit distance based cost as the mathematical formalism to determine optimality of atom mappings. We continue by proposing a compact single-graph representation of reactions using the atom mappings. We investigate the utility of the new representation in a reaction function classification task, where a descriptive category of the reaction’s function is predicted. To facilitate the prediction, we introduce the first feasible path-based graph kernel, which describes the reactions as path sequences to high classification accuracy.
منابع مشابه
Theoretical study of magnetic susceptibility and optical activity of small molecules containing one chiral center
In the first part of this work, correlation between optical activity and elements of magnetic susceptibility tensor (MST) for five classes of model small molecules containing a single chiral center has been studied using quantum computational techniques at DFT-B3LYP level of theory with 6-311G basis set. Several molecular properties are used to reduce the MST elements prior to the examination o...
متن کاملInvestigation of the Molecules Obtained from Marijuana: Computational Study of Spectral, Structural and Docking
There are many chemical molecules whose names are Cannabigerol (CBG), cannabidol (CBD), cannabichromene (CBC), tetrahydrocannabivarin (THCV), cannabigerovarinic acid (CBGV) and cannabidiolic acid (CBDA) derived from Marijuana. Theoretical methods were used to compare the chemical and biological activities of the six major molecules. Molecules were compared with their chemical activities using m...
متن کاملP122: Small Molecules as Chemical and Pharmacological Tools for Neuroinflammatory Diseases Treatment (with Emphasis on Multiple Sclerosis)
Multiple Sclerosis (MS) is a neuroinflammatory disease resulting in degeneration of the myelin sheaths and death of oligodendrocytes. So far, several strategies have been introduced to control the disease. Treatment with small molecules is one of the strategies that have recently attracted the attention in the scientific community. These molecules that target epigenetic and other cellular proce...
متن کاملOn Two Methods for Computing the Non-Rigid Group of Molecules
In this paper, two methods are described, by means of which it is possible to calculate the non rigid group of molecules consisting of a number of XH3 groups attached to a rigid framework. The first method is a combination of the wreath product formalism of Balasubramanian and modern computer algebra and the second method is a computational approach by using group theory package GAP. We apply t...
متن کاملDoes One-third Scheme of PBE0 Functional Dominate Over PBE0 for Electronic Properties of Transition Metal Compounds?
The one-third paradigm of PBE0 density functional, PBE0-1/3, has shown to be a successful method for various properties. In this paper, the applicability of PBE0-1/3 is put into broader perspective for transition metals chemistry. As a comparative study, the performance of PBE0 and PBE0-1/3 has been assessed for geometries and vibrational frequencies of some transition metal hydrides and transi...
متن کامل