Molecular dynamics simulations

Slides:



Advertisements
Similar presentations
You are all made of very tiny atoms ©. The atoms are so tiny that they can hardly be seen with the most powerful microscopes ©
Advertisements

HOW THE WORLD WORKS, ACCORDING TO CHEMISTRY Part 8a.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 2: The chemical basis of life.
Biochemistry. Basic Elements 99% of all living things are: Sulfur (S) Carbon (C) Hydrogen (H) Nitrogen (N) Oxygen (O) Phosphorus (P)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The chemical basis of life.
Figure 2.1 The hierarchy of biological order from atom to organism.
4.2 Carbon compounds and cells Life as we know it is carbon based. A carbon atom can form chemical bonds with other carbon atoms in long chains or rings.
{ Levels of organization What do you find inside of a cell? Organelles Organelles What makes up those organelles?
Sea turtles Current Biology
4.2 Carbon compounds and cells
Activity 17: Modeling Molecules
Philippe Derreumaux, Tamar Schlick  Biophysical Journal 
Volume 8, Issue 9, Pages R177-R185 (September 2000)
Indi Trehan, Federica Morandi, Larry C Blaszczak, Brian K Shoichet 
Laminopathies: Too Much SUN Is a Bad Thing
Effect of Trehalose on a Phospholipid Membrane under Mechanical Stress
Pedro R. Magalhães, Miguel Machuqueiro, António M. Baptista 
Volume 7, Issue 9, Pages (September 2000)
Lab Shapes of Molecules.
Olivier Fisette, Stéphane Gagné, Patrick Lagüe  Biophysical Journal 
Biomolecules Nutrient Sort Biology 12.
Generalizable Learning: Practice Makes Perfect — But at What?
Steered Molecular Dynamics Studies of Titin I1 Domain Unfolding
Zooming in Plants.
Β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water  Xiongwu Wu, Bernard R. Brooks  Biophysical.
Molecules of Life: Macromolecules
Light-Harvesting Complex: Rings of light
Is green tea good for HIV-1 infection?
Visual Attention: Size Matters
Drawing Chemical Formulas Activity
Mark Ultsch, Nathalie A Lokker, Paul J Godowski, Abraham M de Vos 
Ubiquitin Recognition by the Human TSG101 Protein
Liqun Zhang, Susmita Borthakur, Matthias Buck  Biophysical Journal 
Satoko Ohta, Mohammad Taufiq Alam, Hideo Arakawa, Atsushi Ikai 
Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin
Major Organic Compounds
Sea turtles Current Biology
Can you do the following?
It’s all about the constraints
Volume 15, Issue 13, Pages R483-R484 (July 2005)
Volume 18, Issue 10, Pages (October 2011)
A Drug-Drug Interaction Crystallizes a New Entry Point into the UPR
Ronen Zangi, Marcel L. de Vocht, George T. Robillard, Alan E. Mark 
Dynamic Helix Interactions in Transmembrane Signaling
BRIGHT Teacher Molecule™
Volume 77, Issue 1, Pages (July 1999)
Volume 6, Issue 10, Pages (October 1998)
Morphology of protein–protein interfaces
Volume 20, Issue 9, Pages (September 2013)
The Cell Biology of Genomes: Bringing the Double Helix to Life
Tight junctions: Closing in on the seal
Matter in your body Elements Fundamental units of matter
Volume 7, Issue 6, Pages R147-R151 (June 2000)
Protein Dynamics: Moore's Law in Molecular Biology
Binding Affinity and Interaction of LL-37 with HLA-C
Amedeo Caflisch, Martin Karplus  Structure 
Karina Kubiak, Wieslaw Nowak  Biophysical Journal 
Histones and histone modifications
Volume 14, Issue 6, Pages (June 2006)
Shapes.
Alec E. Hodel, Paul D. Gershon, Florante A. Quiocho  Molecular Cell 
T Barrett, CG Suresh, SP Tolley, EJ Dodson, MA Hughes  Structure 
Molecular Similarity Analysis Uncovers Heterogeneous Structure-Activity Relationships and Variable Activity Landscapes  Lisa Peltason, Jürgen Bajorath 
Volume 98, Issue 10, Pages (May 2010)
Bonding: General Concepts (cont’d)
Stereoimage of three independent docking simulations of the interaction between clopidogrel acyl 1-β-d-glucuronide and the active site of CYP2C8. Stereoimage.
Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a.
Distribution of Halothane in a Dipalmitoylphosphatidylcholine Bilayer from Molecular Dynamics Calculations  Laure Koubi, Mounir Tarek, Michael L. Klein,
Stanley J Watowich, John J Skehel, Don C Wiley  Structure 
Molecular Dynamics Simulation of a Synthetic Ion Channel
Presentation transcript:

Molecular dynamics simulations Bruce Tidor  Current Biology  Volume 7, Issue 9, Pages R525-R527 (September 1997) DOI: 10.1016/S0960-9822(06)00269-7 Copyright © 1997 Terms and Conditions

Figure 1 A computer-simulated time-lapse image (in the manner of Edgerton) of a portion of a protein. Oxygen atoms are red, carbon atoms green, nitrogen atoms blue, sulfur atoms yellow, and hydrogen atoms capable of participating in hydrogen bonds are white. Solvent water molecules (red and white V-shaped molecules) exhibit the largest motions, while protein groups undergo smaller overall motions on a short time scale. © Bruce Tidor Current Biology 1997 7, R525-R527DOI: (10.1016/S0960-9822(06)00269-7) Copyright © 1997 Terms and Conditions