Basic procedure for MD simulations

Slides:

Advertisements

Similar presentations

Rosetta Energy Function Glenn Butterfoss. Rosetta Energy Function Major Classes: 1. Low resolution: Reduced atom representation Simple energy function.

Advertisements

Computational methods in molecular biophysics (examples of solving real biological problems) EXAMPLE I: THE PROTEIN FOLDING PROBLEM Alexey Onufriev, Virginia.

Structure Visualization UCSF Chimera José R. Valverde CNB/CSIC © José R. Valverde, 2014 CC-BY-NC-SA.

The total energy as a function of collective coordinates, ,  for upright and tilted structures are plotted. Two types of frequency spectrum are calculated:

AMBER. AMBER 7 What is AMBER? –A collective name for a suite of programs that allow users to carry out molecular dynamic simulations. –And a set of molecular.

CH24 in Robotics Handbook Presented by Wen Li Ph.D. student Texas A&M University.

Tertiary protein structure viewing and prediction July 1, 2009 Learning objectives- Learn how to manipulate protein structures with Deep View software.

Evaluation of Fast Electrostatics Algorithms Alice N. Ko and Jesús A. Izaguirre with Thierry Matthey Department of Computer Science and Engineering University.

2. Modeling of small systems Building the model What is the optimal conformation of a molecule? What is the relative energy of a given conformation? What.

Tertiary protein structure viewing and prediction July 5, 2006 Learning objectives- Learn how to manipulate protein structures with Deep View software.

Protein Primer. Outline n Protein representations n Structure of Proteins Structure of Proteins –Primary: amino acid sequence –Secondary:  -helices &

Computational Biology, Part 10 Protein Structure Prediction and Display Robert F. Murphy Copyright  1996, 1999, All rights reserved.

Physics of Protein Folding. Why is the protein folding problem important? Understanding the function Drug design Types of experiments: X-ray crystallography.

High Throughput Processing of the Structural Information of the Protein Data Bank Zoltán Szabadka, Vince Grolmusz Department of Computer Science Eötvös.

The Importance of Protein Flexibility in Protein-Ligand Docking Jennifer Metzger October 15th, 2008.

Dealing with Non-standard Residues in AMBER

Protein Structure Prediction and Analysis

Bioinf. Data Analysis & Tools Molecular Simulations & Sampling Techniques117 Jan 2006 Bioinformatics Data Analysis & Tools Molecular simulations & sampling.

BOOK CHAPTER R. Mukherjee and T.C. Bishop. “Nucleosomal DNA: Kinked, Not Kinked, or Self-Healing Material?” Frontiers in Nucleic Acids, Chapter 5, pp 69–92.

Computational Structure Prediction Kevin Drew BCH364C/391L Systems Biology/Bioinformatics 2/12/15.

Computer-Assisted Drug Design (1) i)Random Screening ii)Lead Development and Optimization using Multivariate Statistical Analyses. iii)Lead Generation.

DockoMatic: Automated Tool for Homology Modeling and Docking Studies DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking Tutorial.

Development of Software Package for Determining Protein Titration Properties By Kaila Bennett, Amitoj Chopra, Jesse Johnson, Enrico Sagullo.

Maestro environment in practice Balázs Jójárt. Today …  how to draw a small molecule && make nice pictures  how to handla large molecule, like a protein,

What are proteins? Proteins are important; e.g. for catalyzing and regulating biochemical reactions, transporting molecules, … Linear polymer chain composed.

CRB Journal Club February 13, 2006 Jenny Gu. Selected for a Reason Residues selected by evolution for a reason, but conservation is not distinguished.

A new Approach to Structural Prediction of Proteins Heiko Schröder Bertil Schmidt Jiujiang Zhu School of Computer Engineering Nanyang Technological University.

Beckman Institute, UIUCNIH Resource for Biomolecular Modeling and Bioinformatics Molecular Dynamics Method 1 James Phillips Theoretical.

 Four levels of protein structure  Linear  Sub-Structure  3D Structure  Complex Structure.

CZ5225 Methods in Computational Biology Lecture 4-5: Protein Structure and Structural Modeling Prof. Chen Yu Zong Tel:

1 P9 Extra Discussion Slides. Sequence-Structure-Function Relationships Proteins of similar sequences fold into similar structures and perform similar.

Protein Molecule Simulation on the Grid G-USE in ProSim Project Tamas Kiss Joint EGGE and EDGeS Summer School.

MSDmotif 1 Adel Golovin Protein Site and Motif search Biosapiense network of excellence.

E-science grid facility for Europe and Latin America E2GRIS1 André A. S. T. Ribeiro – UFRJ (Brazil) Itacuruça (Brazil), 2-15 November 2008.

Bulk Model Construction and Molecular Replacement in CCP4 Automation Ronan Keegan, Norman Stein, Martyn Winn.

A Technical Introduction to the MD-OPEP Simulation Tools

Module 3 Protein Structure Database/Structure Analysis Learning objectives Understand how information is stored in PDB Learn how to read a PDB flat file.

Protein Tertiary Structure. Protein Data Bank (PDB) Contains all known 3D structural data of large biological molecules, mostly proteins and nucleic acids:

EBI is an Outstation of the European Molecular Biology Laboratory. Quaternary Structure.

NIH Resource for Biomolecular Modeling and Bioinformatics Beckman Institute, UIUC Molecular Dynamics Method 2 Justin Gullingsrud.

1.  Introduction  STARTING a SPDB view Session  Basic SPDB view Commands  Advanced SPDB view Commands  Ending a SPDB view Session 2.

Polish Infrastructure for Supporting Computational Science in the European Research Space EUROPEAN UNION Examining Protein Folding Process Simulation and.

Structural classification of Proteins SCOP Classification: consists of a database Family Evolutionarily related with a significant sequence identity Superfamily.

HANDS-ON ConSurf! Web-Server: The ConSurf webserver.

Marlou Snelleman 2012 Protein structure. Overview Sequence to structure Hydrogen bonds Helices Sheets Turns Hydrophobicity Helices Sheets Structure and.

HANDS-ON ConSurf! Web-Server: The ConSurf webserver.

Instructor: Elon Yariv – PDB founded with 7 X-ray structures – 102,318 X-ray, 11,256 NMR & 933 EM structures.

The Construction of a Viscinal Ice Slab for Molecular Dynamics Simulations Alicia Burns 1* and Steven Neshyba 1 1 University of Puget Sound, Tacoma, WA.

Sequence: PFAM Used example: Database of protein domain families. It is based on manually curated alignments.

Computational Structure Prediction

March 21, 2008 Christopher Bruns

ZEPHYR + GROMACS José R. Valverde CNB/CSIC

Computational design of protein function

The Standard Analysis chain

Visualization with VMD

Protein Structure Prediction and Protein Homology modeling

Structure Prediction dmitra 11/18/2018.

Intro to Molecular Dynamics (MD) Simulation using CHARMM

Analysis of crystal structures

Ligand Binding to the Voltage-Gated Kv1

Volume 19, Issue 5, Pages (May 2017)

What DNA sequence codes for this chain of amino acids...?

Bioinformatics Unit, Life Science Faculty, TAU

Feng Ding, Douglas Tsao, Huifen Nie, Nikolay V. Dokholyan Structure

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Fig. 5 Classical MD simulations.

Presentation transcript:

Basic procedure for MD simulations Yaozong Li Nov. 20, 2017

Protein preparation 1 Solvating the system Ionizing 2 Minimization 3 MD simulation 4

1. Protein preparation Download original PDB file (1p4o, chain A) Extract the target structure Fix the structure (check the sequence, add hydrogen, regulate side chains of protein residues, make up the missing parts) IGF-1RK Apo (PyMoL Show) Chem. Sci., 2017, 8, 3453–3464

Protonation states rotation

2. Solvating and ionizing the system (PyMoL Show)

3 & 4. Minimization & MD simulation Configuration file: Structure (psf) Coordinates (PDB) Parameters Interactions (vdW & electrostatic) Temperature & pressure control Periodic boundary conditions

5. Parameterization of small molecules An easy way: search parameter databases (e.g., https://cgenff.paramchem.org/)

Example J Comput Chem. 2010 Mar;31(4):671-90.