Lac repressor recognizing the DNA operon. More..
Announcement - Two-Day Workshop:
Practical Protein 3D Structure Visualization and Structural Bioinformatics

Group I (filled): Monday June 11 & Thursday June 14, 2012.
Group II (filled): Monday June 18 & Thursday June 21, 2012.
University of Massachusetts, Amherst

Integrated Sciences Building 321, 9:00 AM - 1:00 PM each day.
Limited to 15 participants per group.

taught by Eric Martz (UMass, Amherst)
principal author of FirstGlance in Jmol, and MolviZ.Org
and team member of Proteopedia.Org.

To register, please email
Bringing your own laptop computer is encouraged (details).
Anti-Alzheimer's drug analog (*) interaction with acetylcholinesterase (1gpk, cf. 1vot: Dvir et al./Sussman, 2002).

Level: This course is designed for faculty, postdocs, research staff and graduate students in biological/biochemical sciences. No prior experience with protein 3D visualization or structural bioinformatics is necessary.
Objectives: Participants will use free, genuinely user-friendly software for visual investigation of 3D molecular structures of proteins, nucleic acids, and their interactions with each other and with ligands, substrates, and drugs, and protein evolutionary conservation. Hands-on experience will be largely with molecules of each participant's choosing. We will touch on the challenges of crystallography, uncertainty in electron density maps, and the nature of 3D structure data ("PDB files"). Participants will learn how to create interactive, on-line customized molecular structure scenes useful in teaching, research, and journal supplementary materials; as well as publication-quality molecular images, and rotating molecules in Powerpoint slides.

Potassium channel (1R3J) showing membrane surface planes (from OPM).
Participants will gain hands-on computer experience with:
  • Visual exploration of the 3D structures of macromolecules, such as proteins bound to ligands or nucleic acids.
  • Finding protein structures related to your research, how they are determined, and how much of the genome (and is not) known.
  • Obtaining homology models with an automated server (Swiss-Model) when a crystallographic structure is not available.

  • Seeing noncovalent bonds between a ligand and protein, and measuring interatomic distances.
  • Finding amino acids or sequence numbers of interest.
  • Locating patches conserved in evolution, and regions of rapid mutation.
  • Visualizing specific oligomers, and their subunit interactions.
  • Evaluating the quality of a molecular model, and finding gaps in protein chain models.

  • Creating and sharing customized, rotatable/zoomable online 3D molecular structure-function explanations in the Proteopedia.Org wiki.
  • Creating static publication-quality molecular images for papers or slides.
  • Creating rotating or animated molecular views ready to paste into Powerpoint slides or websites.

Major histocompat- ibility protein (MHC I 2VAA): evolutionary conservation and variability from ConSurf. More..
Software & Ease of Use: Participants will use powerful, state of the art, free, open-source software designed for ease of use. This software works equally well on Microsoft Windows, Macintosh OS X (Intel or PPC), or linux, and requires no installation. Learning specialized scripting command language, such as needed for PyMol, Chimera or RasMol, is not necessary. Most of the resources use the Jmol java applet.

Computers: Participants are encouraged to bring their own laptop computers (Windows, Mac OSX, or linux). However, iMac's are also available in the workshop room. (If your laptop does not have wireless networking, please bring a network cable -- if your laptop is not registered with UMass OIT, then ADVANCE REGISTRATION is required: )

What is Not Covered: Molecular model building, and changing molecular models (mutation, energy minimization). Making animations (morphs) of conformational changes. Professor Martz (Hasbrouck 121) will be available for private appointments to help with specific projects and methods not covered in the workshop.

Contents in Detail: For the complete agenda, please see the course Syllabus.