SBGrid Consortium - News and Events

We completed the transition of Hogle laboratory (BCMP, HMS) to the core network for Center for Molecular and Cellular Dynamics at HMS. The transition facilitates further integration of structural biology computing at Harvard Medical School and creates a large SBGrid managed network segment. OSX computing infrastructure in Hogle laboratory was initially designed by SBGrid senior software architect, David Gohara, and has been recently highlighted on the Apple web site: http://www.apple.com/science/profiles/harvardmed/

SBGrid welcomes our newest member, Dr. Moonsoo Jin. Dr. Jin obtained his Ph.D. at MIT where he studied cartilage cell and matrix mechanics. He completed his postdoctoral training under Tim Springer at Harvard Medical School. There, he studied cell adhesion molecules like integrin and ICAM-1 (http://www.pnas.org/cgi/content/abstract/103/15/5758). His current research takes place at Cornell University, Department of …

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We would like to remind you that our 144 CPU computational grid is available to the SBgrid community through the General User Program at no extra charge. Our Research System Architect, Ian Levesque, now maintains the Grid. Proposals are considered through a web-based system for submission, review, and allocation. All members of SBGrid are qualified to apply. Please visit www.sbgrid.org/gup to submit your proposal. This month’s awardees include Josh Campbell for docking calculations (Harrison, Gaudet and Miller laboratories), and Stefan Raunser (Walz laboratory) for EM 3D-classification and angular assignment by maximum-likelihood refinement.

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The new software will be available on your computers on Saturday, September 9th.

The following applications will be updated in the process:

CCP4 to version 6.0.1 – CCP4 version 6.0 is the most recent major release of the CCP4 software suite and was made in February 2006. A current patch release 6.0.1 was made to fix a number bugs, however there were no major changes to functionality.

coot to version 0.1.1. This update in addition to bug fixes adds a nucleotide builder module. See the release notes for full listings.

New software:

Madbend – a program for calculating the curvature of nucleic acids developed by Tamar Schlick’s group at New York University. The manual for the application is available in /programs/arch/madbend directory. Requested by Daniel Panne, Harrison Lab. …

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Dear Readers,

Welcome to the first of our monthly newsletters. You are receiving this newsletter because your laboratory or institution subscribes to SBGrid services. It is our hope that through this medium we will provide you with useful and relevant information about SBGrid. In this issue you can learn more about access to SBGrid core computational clusters, a molecular visualization class in Boston, our newest member lab at Cornell University, transition of an HMS laboratory to the SBGrid core infrastructure, enhancements on our website, and finally software upgrades and updates that are scheduled for Friday, September 9th.

Finally, as always, we remind our readers that they are welcome and encouraged to report any software bugs utilizing SBGrid Bug Tracker (www.sbgrid.org/bugs).

Kind regards,

Piotr Sliz
Group Leader …

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Want to interpret protein and DNA structures but have no background in structural biology? Need to make publication-quality figures of protein structures and molecular animations for your seminars? This is a hands-on nanocourse for you. We will introduce you to SBGrid Suite – a complete applications environment for structural biology. After learning basic UNIX commands and an introduction to the RCSB Protein Data Bank file formats you will scrutinize the structure of clathrin coats, 7.7 MDa hexagonal barrel particles. We will visualize macromolecular properties including side-chain interactions, electrostatic potential, hydrophobicity and solvent accessible area, as well as perform secondary structure identification and structure quality verification. You will also learn how to transform coordinates, assemble biological units using symmetry …

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