An introduction to docking The docking process involves the prediction of ligand conformation and orientation (or posing) within a targeted bi nding site (BOX 1).In ge neral,there are two aims of docking studies: accurate structural modelling and correct prediction of activity.However,the identifi-cation of molecular features that are • Rigid body docking using a shape-based approach: - random generation of poses within active site - use of Gaussian functions to represent atoms - Use of Gaussian docking functions (combines overlap between ligand with protein atoms and area intersection) and a Quasi-Newton rigid body optimization algorithm to place ligand and select poses What does this practical cover? We will first look at the protein structure (PDB ID: 1HSG) used in the molecular dynamics practical in a bit more detail. We will then try to dock couple of drug molecules into the binding site to see how well docking can reproduce the binding pose. In silico analysis and molecular docking studies of potential angiotensin-converting enzyme inhibitor using quercetin glycosides Syed Aun Muhammad and Nighat Fatima 1 Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan Docking Methods Thomas Funkhouser Princeton University CS597A, Fall 2005 Review Goal: Introduction Scoring functions • Molecular mechanics • Empirical functions • Knowledge-based Searching poses & conformations • Sy st em ai cr h • Molecular dynamics Peptide deformylase (PDF), Antibacterial, Thiazides, Molecular docking, Autodock 4.2. INTRODUCTION diuretics, used for treat. An increase in frequency of antibiotic resistance has been observed in broad range of pathogenic bacterial strains since past few decades. Emergence of such resistance becomes more severe when it In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. Molecular Docking. VIRTUAL SCREENING. Anjaney Sharma INTRODUCTION Docking is an attempt to find the best matching between two molecules. A more serious definition. Docking is a method which predicts the preferred orientation of one ligand when bound in an active site to form a stable complex. An introduction into "Docking" and "Molecular Dynamics simulations" Univ. Ass. Dipl.-Ing. (FH) Dr. scient. med. Bernhard Knapp Center for Medical Statistics, Informatics and Intelligent Systems Department for Biosimulation and Bioinformatics Medical University of Vienna / AKH (General Hospital) bernhard.knapp@meduniwien.ac.at ligand Docking The geometric filtering. Structural Bioinformatics 2004 automated molecular docking of flexible molecule databases, J. Comp. Aided Mol. Design, 15, 411—428, (2001). Allows introduction of electrostatics as the CHAPTER -5 MOLECULAR DOCKING STUDIES 5. Molecular docking studies Brief Introduction of the docking software used in the study 5.4.1. Cambridge Crystallographic Data Centre (CCDC) GOLD GOLD (Genetic Optimization for Ligand Docking) (Jones.G et al. Introduction to Schrodinger's Software Yuk Sham / Feng Chen Center for Drug Design Ligand Docking Jaguar - Quantum Mechanics Liaison - Predicts Binding Affinity LigPrep - 2D to 3D Ligand Convers