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Introduction to Computer Methods in Molecular Structure

Introduction to Computer Methods in Molecular Structure.

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Introduction to Computer Methods in Molecular Structure

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  1. Introduction to Computer Methods in Molecular Structure The objective of this set of lectures and laboratories is to provide students with a basic knowledge about some of the computational resources related to studies in the field of computational biology, and to enable them to use some of these tools.

  2. Overview • Molecular Graphics Software • for publication, visual presentation, and analysis • Structure and Dynamics Prediction • needed for understanding function in • protein chemistry • protein – DNA interactions • protein – ligand binding • intelligent structure based drug design

  3. Molecular Graphics Software • Rasmol/Raswin • for viewing protein structures and producing publication figures • Protein Explorer • uses Rasmol in a user-friendly wrapper • VMD (Visual Molecular Dynamics)‏ • for viewing and analysing molecular dynamics simulations and building dynamics movies

  4. Structure and Dynamics Prediction • Prediction of protein structure • X-ray and neutron diffraction, and NMR, provide experimentally known 3D structures. • Ab initio: Go to 3D structure from sequence only. • Comparative modeling (comparisons to knowns). • Prediction of dynamic (function) properties • Can use known 3D structures • Quantum Mechanics (QM)‏ • Molecular Mechanics (MM)‏

  5. Quantum Mechanics • required for covalent bond breaking-making • first principles approximate solutions to the Schrödinger wave equation, ab initio • not practical for large proteins, expensive • used to calculate parameters for Molecular Mechanics potential functions (see below)‏ • used in combined QM/MM methods for large proteins (Gaussian ONIOM)‏ • Density Functional Theory (DFT) methods can be applied to some proteins and DNA (CP2K and Quickstep)‏

  6. Molecular Mechanics • not useful for making and breaking bonds • calculates molecular energy using classical potential functions with theoretical (from QM) and empirical parameters • There are many MM force fields available. • used to refine predictions of 3D structure in • Modeler • SWISS-MODEL (accessed by Deep View)‏ • Tinker

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