Dear Consortium Members and Affiliates,
As we tramp through the leaves that litter the ground and continue our march toward months of cold, we aim to keep the intellectual fires burning with many opportunities for learning. To that end we have a lineup of webinars to take us through March, details on the next Schrodinger Working Group, a software release extraordinaire, with 25 updates and 10 new applications, a glimpse into the life and work of contributing software developer Klaus Schulten, a new job posting from one of our member labs, two new labs to welcome, and highlights from some of our members' publications.
In October SBGrid PI, Piotr Sliz provided updates on the SBGrid research environment at U Virginia, UCSD, and PDB/San Diego. Thanks to Profs. Kevin Corbett and Wladek Minor for coordinating those visits. Our Structural Biology Data Grid (data.sbgrid.org) effort was also presented during a recent HMMI workshop on Challenges in Crystallography, which was held at the Janelia Research Campus and organized by SBGrid member Tamir Gonen. Groups that are interested in learning more about SBGrid infrastructure can contact us to schedule a visit.
Graeme Winter from Diamond Light Source is up next in our webinar series. He'll give a presentation on DIALS (Diffraction Integration for Advanced Light Sources) on Nov 17th. We've also posted the September HADDOCK webinar on YouTube and fleshed out our webinar lineup for the next several months, so please mark your calendars for the following dates:
- Dec 1, 2015: Ivet Bahar from the University of Pittsburgh on the ProDy python package for protein structural dynamics analysis.
- Jan 26, 2016: Roberto Tejero on PDBStat, an application for analysis, conversion, and manipulation of coordinate and constraint files.
- Feb 9, 2016: James Foadi of Diamond Light Source on BLEND (in the CCP4 Suite), a program for the management of multiple datasets.
- Mar 15, 2016: Raj Pannu of Leiden University on CRANK2 (in the CCP4 Suite), a pipeline for SAD and MR-SAD data.
The SBGrid technical team has been putting in overtime to push out a backlog of software updates and new additions. There are lots of new toys to explore with 25 updates and 10 new applications:
- Updated applications: 3DNA, ATSAS, Blast+, CCP4MG, Chimera, CS-Rosetta, DSSR, EMAN2, EMBOSS, FASTA, Frealign, Geneious, GROMACS, iMosflm, IMP, MAFFT, NMRPipe, Phenix, PyMOL, Schrodinger, Spider, Unio, XDS, XDSGUI, and XPLOR-NIH.
- New applications: Cryo-EM Tools, d*TREK (free), FRODOCK, FUDA, iMOD (NMA), MISO, ORCA, OpenMM, PDBFixer, SamViewer.
Ever wonder what ballet, theoretical physics, and computational biophysics have in common? Klaus Schulten's dreams, it seems. For a 3rd-string dream, it's worked out ok. Applying theoretical physics to understand biological systems, Schulten has spent over 40 years pushing the envelope to advance our understanding of living systems. Read our webtale for a little history and glimpse into his future plans to simulate the entire living cell.
Our job postings page was recently updated to include an open position in Kevin Corbett's lab at UC San Diego and the Ludwig Institute for Cancer Research. Corbett is seeking a post-doctoral fellow to study multi-subunit protein complexes critical for meiotic recombination and chromosome segregation. Read the full details here and be sure to contact us if you would like to post open positions in your group on the SBGrid website.
We have two new members to welcome this month: Eric Fischer, who is just setting up his lab at Dana-Farber Cancer Institute, and Filipe Maia from Uppsala University, our first member from Sweden. Welcome to our new members!
For the month of September, SBGrid received 2 new citations in member publications. Catherine Drennan's group at MIT reported on a B12-dependent photoreceptor in Nature Nature 2015. 526, 536–541 and Lynne Howell from University of Toronto describes the importance of Pseudomonas aeruginosa Glycoside Hydrolase PslG on Polysaccharide Biosynthesis and Biofilm Formation in the Journal of Biological Chemistry J Biol Chem. 2015.
Over 50 manuscripts were published from SBGrid member labs last month. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- From the laboratory of Tom Walz, formerly at Harvard Medical School, but recently transplanted to Rockefeller U, comes some history on the pitfalls faced when using single-particle EM to study membrane proteins and how technological advances in direct electron detection device cameras are revolutionizing the field. Read more in the journal Microscopy
- A study from Caltech's André Hoelz appears this month in Science and gives us new insight into the nuclear pore complex, which is targeted by many diseases. Building on his previous work describing the atomic structure of the outer ring, Hoelz has now defined the architecture of the inner ring, debunking the belief held by many that this ring is flexible and expandable. Read the full story.
- From our undergraduate desk: Harvard Medical School student Kristen Rodrigues chooses a different member publication to highlight each month on our tumblr page. This month Kristen chose Colorado State University PI Shing Ho's review of halogen bonding in drug design in the Journal of Medicinal Chemistry.
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data along with the PDB record and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
3DNA version 2.2-2015jun09 was pushed out with a new -c1 option in the ‘analyze’ program to calculate six local base-pair step parameters based on consecutive C1'--C1' vectors. The numerical values of this new set of parameters are sensible even for dinucleotide steps involving non-Watson-Crick (such as Hoogsteen) base pairs. The Ruby script x3dna_ensemble analyze and the rebuild program were also refined.
ATSAS version 2.7.0-1 is available for Linux users by version override and includes a number of new programs: 1) sreflex, for flexible refinement of high-resolution structures based on SAXS and normal mode analysis, 2) supalm, for rapid superposition of high and low resolution models using spherical harmonics, 3) datshanum, which gives a quantitative assessment of the useful angular data range, 4) datmow for molecular weight estimation, and 5) SASpy, an ATSAS plugin for PyMOL. Please note that ATSAS is not included in the default installation If you don't have ATSAS, but would like to add it, please follow the instructions here.
CCP4MG 2.10.5 introduces major improvements to PdbView.
Chimera version 1.10.2 fixes code signing for Mac OS X installations, adds support for Gromacs 5 trajectories, and updates the URLs for the PDB2PQR web service at NBCR and for CASTp fetch.
CryoEMTools 20151015 is new to SBGrid and brings a handy collection of software tools known officially as the Toronto Single Particle Cryo-EM Software Tool Collection (rolls right off the tongue). This collection was developedby John Rubinstein at the University of Toronto for the computational analysis of cryo-EM images.
CS-Rosetta is now at version 3.1 and includes the CS-Rosetta Toolbox, which provides useful scripts for preparing, running, and analyzing CS-Rosetta runs.
The open source version of d*TREK is now in the SBGrid collection. The d*TREK suite processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. The free version contains neither the Reqab absorption correction nor the absorption correction written by Higashi. It also does not make any use of collision file information during strategy generation.
DSSR is now at version 1.3.9-2015oct08. You'll notice many changes since we last updated DSSR, including code refinements and refactoring and classification of base-stacking interactions (option --non-pair), along with a new set of "simple" base-pair parameters (Shear, Stretch, Buckle and Propeller, are for structural description only) that are more intuitive for non-canonical bps.
EMAN2 version 2.12 is the new default. This version includes new subtomogram averaging programs, and a faster alignment routine. A new --inputavg option allows users to use one set of particles for alignment and a separate set for reconstruction. The e2refine_split program will split a heterogeneous single map reconstruction into 2 submaps.
For those of you looking for the latest and greatest, we also pushed out the 20151008 nightly build, available with a version override.
EMBOSS version 6.5.7 includes a laundry list of changes exhaustively detailed here.
FASTA was updated to version 36.3.8a, which includes alignment sub-scoring scripts that have been extended to allow overlapping domains. This change requires a modified annotation file format and new annotation scripts are available in the fasta-36.3.8/scripts directory, e.g. ann_pfam_www_e.pl (Pfam) and ann_up_www2_e.pl (Uniprot).
Frealign is now at version 9.11_151013. No additional information is available on this update.
FRODOCK or (Fast Rotational DOCKing) version 1.04 is new to SBGrid and available only for Linux installs. FRODOCK efficiently generates predictions for how two proteins could interact and was produced by Pablo Chacon's lab.
FuDA version 20080728 was added for Linux users only. FuDA (Function and Data Analysis) includes an nmrPipeFit component designed to analyze nD (n>1) NMR correlation spectra. This program is designed for arrayed 2D spectra, such as relaxation experiments and diffusion experiments, and simple 2D and 3D spectra and comes from software developer D. Flemming Hansen.
Geneious was bumped up to version 9.0.2. With this release users can use Golden Gate for one-step cloning of large constructs using any mixture of inputs with existing cut sites or automatically designed primers. There is new RNA-seq and structural variant mapping, an option for VCF export of single-sample variants, the addition of Tadpole - a very fast de novo assembler with very low mis-assembly rate, new support for huge phylogenetic trees, a new scoring strategy for on-target activity for CRISPER, and improvements to read filtering.
GROMACS version 5.1 includes performance improvements to mdrun, added support for OpenCL acceleration and inter-molecular bonded interactions, improved parallel distribution and thread count reporting, new low-level SIMD support, and reorganized documentation.
iMOD of another flavor was just added to the SBGrid collection. To distinguish it from the existing iMOD we're calling it iMOD (NMA), now at version 1.3. This toolkit performs Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories, and Monte-Carlo simulations can be easily carried out at different resolution scales.
iMosflm was updated to version 7.2.1. With this version users can process images from the Pilatus detector on beamline I24 at Diamond and partial support is available for the Pilatus 300K detector sold with Stoe four-circle goniostat (with detector in symmetric setting). You'll also notice that contrast limits were increased to allow changes with many hot pixels.
IMP version 2.5.0 includes two new command line tools: multi_foxs, for enumeration and scoring of multi-state models against SAXS profiles, and ligand_score_multiple, which acts similarly to the existing ligand_score tool but scores each ligand pose generated by docking software (such as PatchDock). IMP also now allows multi-state modeling of the histidine kinase, PhoQ and determination of the molecular architecture of the 40S•eIF1•eIF3 translation initiation complex.
MAFFT, is now at version 7.245 for Mac only. This update fixes a bug in the combination of --addfragments and --reorder, places remote homologs at the end of the output, changes the parameters for E-INS-i, improves the --merge option speed, adds two new options, --keeplength and --mapout, which work with --add, --addfragments or --addfull.
MISO version 0.5.2 was added to the SBGrid software stew as a standalone application from Yarden Katz at MIT (formerly it was included only as a python module). MISO is an application for probabilistic analysis and design of RNA-Seq experiments for identifying isoform.
NMRPipe version 20150928 is the new default. No release notes are available.
OpenMM, also new to SBGrid, is at version 6.3.0. OpenMM emanates from Vijay Pande's group at Stanford and is a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
ORCA version 3.3, is another new tool added to our install. ORCA, from Frank Neese's lab at the Max-Planck Institute, is an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with a specific emphasis on spectroscopic properties of open-shell molecules.
PDBfixer version 20151011 is yet another new tool at SBGrid from Vijay Pande's group at Stanford. PDBFixer fixes problems in Protein Data Bank files prior to simulation. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, converting non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.
Phenix version dev-2194 is now available via a version override.
PyMOL version 18.104.22.168. is mostly a code refactored release.
SamViewer version 14.05 - also new to SBGrid - is a 2D image display and analysis program, specifically designed for single-particle EM. Follow the SamViewerr link for more information on this application from Maofu Liao's group.
With Schrodinger version 2015 - 3 OPLS3 is the new default force field for most applications. You'll also see improved protein and nucleic acid force fields, new macrocycle support in Force Field Builder. A new custom reaction repository is available for Covalent Docking and from the command line users can now use Glide positional, H-bond, and torsional constraints in docking experiments. Atom and pharmacophore-based screening are 2x faster while pure shape screening is 20% faster. For Molecular Dynamics you can now perform free energy perturbations between two ligands with the new Ligand FEP interface and take advantage of Viparr support for Charmm36 protein parameters. In Protein X-Ray Refinement users can restrict the charge state for specified residues in the polish script and benefit from improved maps generated from coordinates with ANISOU records.
Spider was updated to version 22.10 for Linux.
Unio was updated to version 20111221.
XDS version 20151015 has many performance imprvements along with a new input parameter, NUMBER_OF_IMAGES_IN_CACHE=, in XDS.INP, for explicit user control of the cache size, a simplified method for calculating the initial value of the mosaicity, a restriction to a positive multiple of 0.0001 degrees for the value of the input parameter for OSCILLATION_RANGE=, and error correction in XSCALE.
XDSGUI was updated to version 20150526.
XPLOR-NIH version 2.4 offers two new helper programs: calcPSol, to calculate solvent PREs, and slurmXplor, to simplify use with the SLURM batch queuing system. You'll also notice OpenMP acceleration of EEFx and SAXS calculations for the AMD64 architecture.
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.