Dear Consortium Members and Affiliates,
SBGrid would like to announce the availability of new compound databases for docking with Schrodinger's Glide software on the SBGrid cluster. We have used LigPrep to prepare the Harvard Medical School's ICCB-Longwood screening facility's database of roughly 300,000 compounds. This set can be used when submitting jobs on the SBGrid cluster via the command line. In addition to the docking set, we have also generated MOLPRINT 2D fingerprints with Schrodinger's Canvas tool for cheminformatic analysis of these datasets. Further information regarding use of these databases will be provided in an upcoming SBGrid webinar.
Joseph Ho from Academia Sinica is the subject of our March SBGrid Tale. Read about his young lab in Taiwan and the experiences that shaped his philosophy about how to structure his research group.
We had a great turnout for the March PyMOL webinar. If you missed the presentation, you can watch it at your convenience via our webinar archive. Future webinars are scheduled through July (we'll take an August holiday), and include the following:
- March 28th - SBGrid's Paul Sanschagrin will give a short presentation on the new compound databases and fingerprint tools available for use with Schrodinger
- April 18th: Graeme Winter will discuss XIA2, an automated data reduction system
- May 16th: the Richardson Lab will give a presentation on ERRASER, a thorough RNA backbone correction system
- June 13th: learn about CAVER, a tool to analyze and visualize tunnels and channels in protein structures
- July 11th: the topic will be Jalview, a multiple sequence alignment editor written in Java
All of these dates are included on SBGrid's google calendar.
Upcoming Structural Biology Conferences
Registrations are being accepted through March 27th for The New England Structural Biology Association's upcoming meeting "Protein Misfolding and Rare Genetic Diseases: From Human Genetics to Drug Discovery" to be held at Bentley College in Massachusetts on March 29th. Follow these links to register or for more information on sponsorship opportunities.
The 11th annual Analytical Ultracentrifugation and UltraScan workshop is scheduled for May 29th - June 4th 2013 at the University of Texas Health Science Center in San Antonio. With only 20 seats a available on a first-come, first-served basis, please be sure to secure your seat and register without delay.
The software update on February 26th included new versions of SHELX, DSSP, NMR, relax, Avogadro, a PHENIX nightly build, the latest CCP4 update, and one new package: XrayView.
Notable Software Changes
NMR: Relax, a program designed to study the dynamics of proteins or other macromolecules through the analysis of NMR relaxation experiments, was updated from version 1.3.16 to 2.2.0. According to the software developer "this is a major feature and bugfix release that marks the completion of the N-state model analysis implementation. The N-state model allows single structures or ensembles of static structures to be analyzed and compared using residual dipolar couplings (RDCs), pseudo-contact shifts (PCSs), and distance restraints via NOEs. In addition to alignment tensors, the populations or probabilities of each state can be optimized, as well as the position of the paramagnetic center when PCSs are used."
DSSP is an application used to assign secondary structure that was originally developed by Wolfgang Kabsch and Chris Sander. DSSP underwent a major rewrite in 2011. We have upgraded this package to version 2.0.4, which includes a minor change in ligand handling.
PHENIX version 1.8.2 includes dozens of improvements. For the full list please see the Phenix website. Some of the notable changes include expanded support of mmCIF files and several new commands, including phenix.ensemble_refinement, phenix.ligand_pipeline, phenix.sort_hetatms, phenix.cc_star, phenix.pdb_editor, phenix.maximum_entropy_map. The refinement module was modified to include a new method for refining ensemble models, support for LLG maps, optional output of mmCIF style model and data files. A new command phenix.ligand_pipeline is available and combines Xtriage, Phaser, eLBOW, phenix.refine, AutoBuild, and LigandFit to automatically solve protein/ligand complexes. phenix.autobuild now supports rebuilding from a small but accurate part of a model. A new release of Phenix.xtriage will provide merging statistics if unmerged intensities are used as input. Phenix.pdb_editor supports common operations such as chain renaming, renumbering and manipulation of atomic properties.
SHELX was updated to version 2013/2. Several serious problems affecting MRSAD and expansion from an MR model that were present in the last beta-test version 2013/1 have been fixed. Please note that SHELX is only installed for a subset of sites that have completed an additional licensing/registration requirement.
XrayView, 4.1 was added to our software collection. This application is interactive and can be used as an introduction to basic concepts of X-ray diffraction and data collection. The ‘Options’ menu allows users to setup crystal parameters, such as space group, mosaic spread, or resolution. Exercises on Ewald Sphere, crystal alignment, mosaic spread, wavelength, auto rotation, space groups, systematic absences, and synchrotron radiation are included. XrayView was contributed by Prof. George Phillips Jr. formerly at University of Wisconsin-Madison, and now at Rice University. You can type ‘xrayview to start this application.
Avogadro, a molecular editor and visualizer, was upgraded to version 1.1. This beta release offers several new features, such as "growing" small molecules in place of a selected hydrogen atom, searching PubChem for an IUPAC name using the "Molecular Properties" command, chirality inversion, and copying and pasting from a variety of computational chemistry packages. Several Avogradro tutorials are available online.
The CCP4 update includes a few small fixes.
Consortium members new this month include James Hurley from the NIDDK branch of the NIH and Galina Lepesheva from Vanderbilt University. We've also made a new connection at Baylor College of Medicine, with Ming Zhou's relocation from Columbia to Baylor's Department of Biochemistry and Molecular Biology. From the University of Wisconsin-Madison, we welcome 7 new groups: Samuel Butcher, Brian Fox, Hazel Holden, John Markley, Julie Mitchell, Ivan Rayment, and the Biochemistry Core.
Welcome to our new members!
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.