User:Wayne Decatur/NASCE2011

From Proteopedia

Revision as of 19:05, 12 July 2011

General Introduction

• Thanks to the organizers of the NASCE2011
• About me
• Overview of the workshop planned
• Gauge Audience, Adjust plan?

Introduction to Proteopedia

• Main Page
• Sightseeing by way of example "Case Studies" / ""User Narratives"
  • Topics
    • main page--->Ribosome structure, spin, toggles, list, contributors --->page particular section ---> another page green links
    • via search---> The Glutamate Receptor (GluA2) quality, popup, section window
  • Open-ended Gateway
    • learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> Pubmed search result---> 2rh1
      • Firstglance in Jmol
      • Consurf
    • new publication ---> 3rze
      • note where link to 3D structure at Nature publication goes
  • Student aid - Proteopedia:Table of Contents -->Metabolism -->Carbohydrate Metabolism -->Citric Acid Cycle--> Citrate Synthase morphs and reaction steps in second section
  • Lecturing
    • User:Eric Martz/Nucleosomes
    • resources for this workshop as listed under Workshops and Seminars on my user page as Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011
  • Structural Biology Resource
    • X-ray crystallography ---> Quality assessment for molecular models
    • Cation-pi interactions
  • Student Projects
    • Students at UMASS in classes associated with Chemistry-Biology Interface program design presentations for showing on the Molecular Playground
  • Journal Club --> RecG Bound to Three-Way DNA Junction
  • Communicating specific ideas in context of structure --> e-mail a link to a Sandbox, e.g. Sandbox CsrA
  • Group meeting ---> Proteopedia:Workbench, also good for preparing for publication
  • Publications
    • Collaboration with BAMBEd --->Category:Featured_in_BAMBED ----> Ramachandran Plot
    • Interactive 3D Complements

Under the Hood

• Wiki implementation, very specialized
  • references
    • Create a page for example with references
  • other technical aspects related to Jmol and other media
• Jmol

Jmol

• Jmol
  • The Application
  • The Java Applet - Demonstration with Human Follicle-Stimulating Hormone Complexed with its Receptor
• Advanced Options
  • Console
  • Compare Command Demonstration
  • Sculpting - Simple example of that here
  • 3D options - Demo with Hormone

The Structure Data

• everything centers around an Atomic coordinate file
• Experimental vs theoretical sources

Protein Data Bank

• over 70,000 X-ray crystallography, NMR, and cryo-EM structures
• about 85% are crystallographic structures
• Isomesh of electron density helps illustrate how crystallographic models get built using a portion of one
• Caveat: Keep in mind these are models - Not all models created equally

Proteopedia

• Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
• User or Sandbox login

Types of Proteopedia pages

• Topic Pages
  • Macromolecular Structures
  • About Macromolecular Structure
• PDB Entry Pages
• User space Pages
• Sandbox Pages
• Workbench Pages
• Interactive 3D Complements (I3DC) - Journal of Biological Inorganic Chemistry
• Administrative
  • How To/Guides
  • Organizational/Table of Contents
  • Main Page - the main gateway

Topic Pages

• Examples of structure pages
  • the ribosome structure; contrast with entry at PDB
  • Hemolysin
    • Quality toggle
    • Popup
  • Citrate Synthase
  • The Glutamate Receptor (GluA2)
    • Proteopedia pages can be exported for offline viewing using the toolbox on the left.
• Information and Resource Collection, as well
  • About Macromolecular Structure
  • Cation-pi interactions
  • Searching

User Pages

• Other users cannot edit pages in this space

PDB Entry Pages

• Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful resources
  • Example 1m10
  • Random Example: 1p3v (PDB 4 digit alphanumeric accession number)
    • Conservation: , explanation, and see also The ConSurf Database and The ConSurf Server Other examples: 4enl or 5cyt

FirstGlance in Jmol

• Views and Convenience buttons
  • How many chains? - Use 3pla
  • Key Resources:
    • Biological Unit
    • Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well

Structural Biology for Non-structural Biologists

• MolviZ "Top 5" by Eric Martz
• Polyview-3D = fancy PyMol views and animations made super easy via a web server with forms.
  • Example - 3pla
  • Makes animations too and/or morphs too with multiple model structures

Proteopedia Page Authoring

• Model of a wiki
• Sandbox - there is a "student" login that can be used by groups for editing these for teaching purposes
• Conveniences
  • Buttons for 3D structure windows and other commonly used items
  • Since a large amount of references are from Pub-Med, PMID all that is needed for references in text, combined with a reference list at end
• Proteopedia:How to Make a Page
• How to edit pages in Proteopedia
• Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol

Proteopedia Scene Authoring

• Proteopedia's Scene Authoring Tools
  • Load a structure 2zi0 or previous scene
  • Set your scene. Undo/Redo features.
  • Save your scene
  • Add the scene to the page
• Try it out and then add and improve. Repeat.

Time permitting

• Advanced scenes/toggles - Human Follicle-Stimulating Hormone Complexed with its Receptor has several examples
• Morphing allows displaying the visual transition between two molecular conformations.
• Pymol to Jmol conversion built into Proteopedia's Scene Authoring Tools
• Jmol works with small molecules too
  • • Works with small molecules too and even can do energy minimization with them
    • Can be used to show chemical reactions
• Recalling the Caveat: Keep in mind these are models -Not only are not all models models created equally, not even all portions of models are created equally

• Assessing structure
  • Resolution noted with a link on each PDB entry page
  • Temperature factors, also see demonstration here
  • Gaps, i.e. missing pieces (see above)

Resources

Macromolecular Visualization

• Eric Martz's recent workshop at his list of workshops.
• Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
• About Macromolecular Structure
• FirstGlance in Jmol is very useful for exploring PDB entries or upload structure files.
• Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate useful views. This effort is building Chime-based Protein Explorer to work with Jmol, and a few features may still not yet work.
• MolviZ "Top 5"
• MolviZ.Org
• Protein Explorer's Glossary
• Jmol Application
• PyMol
• Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
• eMovie,a PyMol plug-in for macromolecular movie-making.

Small Molecule Visualization and Model Kits

• CheMagic Virtual Molecular Model Kit
• The Jmol Interface by Mike Evans at University of Illinois has a model kit interface and easy ways to arrows and items.
• ChemCanvas, an open source chemical diagram editor
• ChemTube3D has interactive animations and structures of molecules and reactions important in chemistry.
• Service allowing young people to look up a molecule and blow it up and put it back together

Topic Pages - Education

• Teaching Strategies Using Proteopedia
• Teaching Scenes, Tutorials, and Educators' Pages

Authoring Scenes and Views in Proteopedia and beyond

• Proteopedia:Video Guide
• Proteopedia:How to Make a Page
• How to edit pages in Proteopedia ? Example 1, example 2, and example 3 of edited topic pages.
• Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
• Proteopedia's Scene Authoring Tools
• Perform basic editing and creation of scenes in your Sandboxes
• Copying FirstGlance Scenes into Proteopedia
• User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
• Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
• Comparison of Jmol tutorial-authoring systems
• Copying FirstGlance in Jmol Scenes into Proteopedia
• Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed here or at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
• Jmol Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
• Jmol Command Reference Manual for advanced scene authoring.
• Jmol Wiki
• Morphing allows displaying the visual transition between two molecular conformations.
• Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.

Modeling

• See the end of Eric Martz's recent workshop syllabus where he covers homology (more accurately, comparative) modeling.
• A Feb. 1st 2011 news item about Yang Zhang and his work.
• Mutating an amino acid in a proteins - here with PyMOL and here with Swiss PDB-Viewer
• Homology modeling
  • Eric Martz's page on Homology Modeling
  • Swiss Model
  • Homology Models Database
  • Modbase -Database of Comparative Protein Structure Models
• Comparative Modeling
  • Zhang Server (I-TASSER)
• Ab Initio and Molecular Dynamics
  • Quark server
  • VMD - Visual Molecular Dynamics

Class Sandboxes