User:Wayne Decatur/UNH BCHEM833 Structural Analysis Workshop Session Fall 2012

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This workshop follows from a class lecture on October 25th by Wayne Decatur. This workshop was originally scheduled for a previous date; however, it was moved to November 8th 2012 due to the University closing October 30th 2012.



Getting Started

  • Location of this resource is featured in slides from lecture on Blackboard
  • Signed up for Proteopedia?
    • There is a student account people without accounts can use for today.
  • Java-capable browser?
  • Optional Software?
  • Selected a interesting protein or complex?
    • Have a PDB id for a pertinent structure?
    • Still need ideas for an interesting structure?
      • Search Pubmed with a topic in which you are interested plus the word "crystal"
      • See sections 11 through 13 of Eric Martz's class syllabus.
      • Still no structure eventually you may want to attempt generating a comparative model at Zhang Server (I-TASSER) as discussed in lecture class

Following up from a question in lecture


  • Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
    • wiki model
    • Help:Getting Started in Proteopedia
    • User or Guest login
    • We encourage you all to become users of any sort. If you become a registered user, you can save information in your userspace regardless of your overall contribution to public spaces.

Types of Proteopedia pages

NOTE: Using the 'Export this page' link found in the toolbox on the left hand side of each Protoepedia page, you can save a version of any page on your computer locally with working structure windows for use when your computer may not be connected to the internet.


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
  • Help:Getting Started in Proteopedia
  • 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

Edit a Protoeopedia Page

  • User or Guest login
  • Go to instructed page
    • Registered users can make a sandbox in their userspace that only they can edit
    • Those on student guest accounts can use the class sandboxes below
  • Edit the wiki-text
  • Save the page
  • View the page
  • View the history

Visualization Tools for today

Initial Views

Jmol, particularly Firstglance in Jmol, more informative than PyMol

Hands-On Analyses and Visualization

  • Measure distance - Try 3sn6 and determine what is the thickness typical cell's lipd bilayer? Or try a meaningful measure on your structure? If curious about thickness, see Orientations of Proteins in Membranes (OPM) database. Specifically see 'Comparison with experimental data' under About OPM.
    • Jmol in FirstGlance or Jmol via Proteopedia's Scene Authoring Tools:
      • Double-click on first atom.
      • Double-click on second atom.
    • PyMol: Two ways

  • Superposition
    • Jmol
    • PyMol
      • 'super' command in Pymol, see here
    • Other options for stream-lined ways may be found here eventually a better interface for the new Jmol ability needs to be implemented, but I am not aware of one yet.

Fancy Images Quickly

  • use POLYVIEW-3D
    • make a publication quality static image (already calculated example that should be good only a few days is here
    • Also works for animations and displaying annotations and interactions
    • Also via the 'Rendering Script' link it can be a crutch in making PyMol images locally because you can download commands that you can paste into PyMol or adapt further
  • use for making an image of buried surface area above

Proteopedia Scene Authoring

  • Proteopedia's Scene Authoring Tools
    • Load a structure 1d66 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.

Available Sandboxes

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Additional resources for interactions and epitopes

Previously we discussed using PDBsum to analyze deposited solved structures (or our own structures upon submission). These are additional resources that perform similar functions and are here as an expansion of that information and follow-up for Polyview-3D which access some of this analyses for visualizing the data:

Zellner H, Staudigel M, Trenner T, Bittkowski M, Wolowski V, Icking C, Merkl R. Proteins. 2012 Jan;80(1):154-68. doi: 10.1002/prot.23172. Epub 2011 Oct 31. PMID: 22038731 [PubMed - indexed for MEDLINE] Has a detailed abstract featuring alternatives: ".... A comparison with SPPIDER, ProMate, and meta-PPISP showed that PresCont compares favorably with these highly sophisticated programs, and that its prediction quality is less dependent on the type of protein complex being considered...."

Huang B, Schroeder M. Gene. 2008 Oct 1;422(1-2):14-21. Epub 2008 Jun 14. PMID: 18616991 [PubMed - indexed for MEDLINE] Related citations

Porollo A, Meller J. Proteins. 2007 Feb 15;66(3):630-45. PMID: 17152079

"One of our goals in this paper is to test the validity of a reported interaction by using structural information about the interacting proteins in a cluster. Our idea is simple: first, find the structures of the two interacting proteins from the PDB [10]. If the experimental structure is not available in the PDB for any of the proteins, we predict its structure by comparative modeling. For comparative modeling, we used both CABS modeling [11] and I-TASSER [12-14]. However, the results shown here come only from using I-TASSER. Once, we have both structures, we dock them to predict the interaction complex. We can repeat this method to verify individual interaction in a cluster." "Methods In the present work the yeast protein-protein interaction network is clustered using a spectral clustering method proposed by us in 2006 and the individual clusters are investigated for functional relationships among the member proteins. 3D structural models of the proteins in one cluster have been built – the protein structures are retrieved from the Protein Data Bank or predicted using a comparative modeling approach. A rigid body protein docking method (Cluspro) is used to predict the protein-protein interaction complexes. Binding sites of the docked complexes are characterized by their buried surface areas in the docked complexes, as a measure of the strength of an interaction."

S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin Nature Protocols, 5, 883-897 (2010). Note: it has 'View the docking solutions in a Jmol structure viewer.', see example run, list calculation of Buried Surface Area.

"i. Add missing atoms including polar hydrogen using CHARMM19 (23) and perform a small round of hydrogen minimization to optimize hydrogen bonding. ii. Calculate the change in solvent-accessible surface area upon binding for each residue’s side-chain" "Output is the values of ΔSASA and FastContact energy for each residue" "For a given protein–protein complex submitted by the user, ANCHOR calculates the change in solvent accessible surface area (ΔSASA) upon binding for each side-chain, along with an estimate of its contribution to the binding free energy (19,20). A Jmol-based tool allows the user to interactively visualize selected anchor residues in their pockets as well as the stereochemical properties of the surrounding region such as hydrogen bonding and charge–charge interactions." Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W407–W411. server: article:

"The size of the protein–RNA interface is estimated by measuring the solvent accessible surface area buried in contact....The interacting surfaces can also be visualized with software plug-in like Jmol" Nucl. Acids Res. (2012) doi: 10.1093/nar/gks535 First published online: June 11, 2012 server: article:

  • Epitopes - see that page for, "An epitope is the portion of the surface of an antigen that binds to an antibody, or the peptide fragment of a protein antigen that binds to the T lymphocyte antigen receptor when presented by the cognate major histocompatibility protein. The best way to identify an antibody epitope is from a crystal structure of the antibody:antigen complex, where the contacts are evident. There are several servers that attempt to predict epitopes." Polyview-3D incorporates visualizing epitopes predicted elsewhere.

Additional Resources

The Future: Jmol (and hopefully, eventually Proteopedia) that works on all mobile devices and tablets, for now it is called JSmol

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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