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

Wednesday June 17 & Friday June 19, 2015.
Integrated Sciences Building 321, 9:00 AM - 1:00 PM each day.
University of Massachusetts, Amherst
Limited to 15 participants per group.

taught by Eric Martz (UMass, Amherst)
principal author of FirstGlance in Jmol ( buttons in the journal Nature), MolviZ.Org,
team member of Proteopedia.Org, and coauthor of the ConSurf Server.

To register, please email
Bringing your own laptop computer is encouraged (details).
  Enolase (4enl; a glycolytic enzyme) evolutionary conservation from ConSurf. Catalytic cleft is at the left. More..

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 bioinformatics is necessary.
Objectives: Participants will use highly 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 publication-quality molecular images, and rotating molecules in Powerpoint slides.

Potassium channel (1R3J) showing membrane surface planes (from OPM).
Participants will gain hands-on 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 sequence numbers or motifs in the 3D model.
  • Locating patches conserved in evolution, and regions of rapid mutation.
  • Visualizing specific oligomers ("biological units"), and their subunit interactions.
  • Evaluating the quality and reliability of a molecular model, and finding gaps in protein chain models.

  • Creating static publication-quality molecular images for papers or slides.
  • Creating rotating or animated molecular views ready to paste into Powerpoint slides or websites.

Anti-Alzheimer's drug analog (*) interaction with acetylcholinesterase (1gpk, cf. 1vot: Dvir et al./Sussman, 2002).
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, or linux, and requires no installation. Learning specialized scripting command language, such as needed for RasMol or PyMol, is not necessary. Most of the resources use Jmol, for which Java is optional.

Computers: Participants should bring their own laptop computers (Windows, Mac OS X, or linux). Internet wi-fi will require a UMass OIT account. Ethernet wire connections require prior registration of your MAC address with the Chemistry Department. Bring your power adaptor: electrical power outlets will be available.

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

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