MOLDEX : A Computer System for Drug Design. 3) Constructing Hypothetical Ligand Molecules
نویسندگان
چکیده
The present work is one of a series describing the research and development of a new computer system for drug design: MOLDEX (MOLecular DEsign X). The main characteristics of the system are the modules for receptor site mapping [1,2,3], the module for molecular three dimensional superposition [4], the module for conformation analysis in solution [5], and the molecular dynamics module [6]. Here we propose a new computer methodology for three dimensional QSAR to assist the construction of more suitable and e ective ligand molecules. The proposed computer module is based on the mapping of the three dimensional characteristics of candidate ligands in two dimensions by a self organizing map (SOM) [7] algorithm. This two dimensional map allows a rapid comparison of the structural, reactivity, energetic as well as electrostatic characteristics of ligands, allowing a more robust process of construction of e ective drugs automatically.
منابع مشابه
Discovery of Novel Glucagon Receptor Antagonists Using Combined Pharmacophore Modeling and Docking
Glucagon and the glucagon receptor are most important molecules control over blood glucose concentrations. These two molecules are very important to studies of type 2 diabetic patients. In literature, several classes of small molecule antagonists of the human glucagon receptor have been reported. Glucagon receptor antagonist could decrease hepatic glucose output and improve glucose control in d...
متن کاملDiscovery of Novel Glucagon Receptor Antagonists Using Combined Pharmacophore Modeling and Docking
Glucagon and the glucagon receptor are most important molecules control over blood glucose concentrations. These two molecules are very important to studies of type 2 diabetic patients. In literature, several classes of small molecule antagonists of the human glucagon receptor have been reported. Glucagon receptor antagonist could decrease hepatic glucose output and improve glucose control in d...
متن کاملMolecular Docking Based on Virtual Screening, Molecular Dynamics and Atoms in Molecules Studies to Identify the Potential Human Epidermal Receptor 2 Intracellular Domain Inhibitors
Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand ...
متن کاملBiological Applications of Isothermal Titration Calorimetry
Most of the biological phenomena are influenced by intermolecular recognition and interaction. Thus, understanding the thermodynamics of biomacromolecule ligand interaction is a very interesting area in biochemistry and biotechnology. One of the most powerful techniques to obtain precise information about the energetics of (bio) molecules binding to other biological macromolecules is isoth...
متن کاملAn Automated Ligand Evolution System using Bayesian Optimization Algorithm∗
Ligand docking checks whether a drug chemical called ligand matches the target receptor protein of human organ or not. Docking by computer simulation is becoming popular in drug design process to reduce cost and time of the chemical experiments. This paper presents a novel approach generating optimal ligand structures from scratch based on de novo ligand design approach employing Bayesian optim...
متن کامل