Protein Crystallization Hits

Over the past two years I've systematically reduced the amount of printed paper in my office as well as in my private life. The idea behind this effort is that 'going digital' with all my documents will make it simpler to store and quickly find information that I need. This is work in progress where the crucial software elements that stuck are Sync Toy (general file housekeeping), PICASA (automatic archiving of images) and Google Desktop (searches everything I have on my PC; yes - I'm a PC).

The most recent addition to this toolset is Mendeley. This is a PDF file organization tool that's devised specifically for researchers to archive, annotate and share their PDF articles. To say the least, I'm very impressed with Mendeley's utility. Within a short period of time Mendeley has helped me to aggregate and organize all of my (currently 642 and growing library of) PDF documents. The functionality goes well beyond a traditional Reference Manager. Features are here, the ones that I like particularly are:

• making notes within PDFs,
• sharing libraries over the web,
• backing up my own collection of articles,
• cross-talk with Zotero (a Firefox-based reference manager),
• cross-platform compatibility (I have Mendeley installed on Windows 7 and on iPhone/iPod touch, and use it via the web browser interface - works seamlessly so far) and
• search functionality.

Here's a quick primer to Mendeley:

Mendeley Teaching Presentation

Mendeley : the best research tool since streak-seeding?

There's even a social media facette too; here's my Mendeley profile - friend me if you'd like: 

Oh - and did I mention that Mendeley is available for free?

Cheers,

Peter

Congratulations to Robert G. Edwards to receiving the 2010 Nobel Prize for Physiology or Medicine. Robert is widely known for inventing and promoting the in vitro fertilization procedure. In a way he has 'fathered' 4 million people.

Not bad.

And here's a toast to Richard Heck, Ei-ichi Negishi and Akira Suzuki for receiving the 2010 Nobel Prize for Palladium-catalyzed couplings in organic synthesis.

I'll keep my fingers crossed for protein structural biology Nobels in 2011.

Cheers,

Peter

The NIH has announced on Sept 30 the members of the third Protein Structure Initiative: PSI:Biology Centers for High-Throughput Structure Determination.

Altogether there are 23 grants for structural biology research totaling up to $290 million over the next five years. This is the list of the centers that are expected to 'produce protein structures for functional studies'.

My   C O N G R A T U L A T I O N S   go to:

Joint Center for Structural Genomics
Principal investigator: Ian A. Wilson, D.Phil., Scripps Research Institute

Midwest Center for Structural Genomics
Principal investigator: Andrzej Joachimiak, Ph.D., University of Chicago

New York Structural Genomics Research Consortium
Principal investigator: Steven Almo, Ph.D., Albert Einstein College of Medicine of Yeshiva University

Northeast Structural Genomics Consortium
Principal investigator: Gaetano T. Montelione, Ph.D., Rutgers University

Center for Membrane Proteins in Infectious Diseases
Principal investigator: Petra Fromme, Ph.D., Arizona State University

Center for Structure of Membrane Proteins
Principal investigator: Robert M. Stroud, Ph.D., University of California, San Francisco

Center for the X-ray Structure Determination of Human Transporters
Principal investigators: Douglas C. Rees, Ph.D., California Institute of Technology; Geoffrey A. Chang, Ph.D., Scripps Research Institute; Michael H.B. Stowell, Ph.D., University of Colorado

GPCR Network
Principal investigator: Raymond C. Stevens, Ph.D., Scripps Research Institute

Membrane Protein Structural Biology Consortium
Principal investigators: Michael G. Malkowski, Ph.D., Hauptman Woodward Medical Institute; Mark E. Dumont, Ph.D., University of Rochester; Michael Wiener, Ph.D., University of Virginia

Membrane Protein Structures by Solution NMR
Principal investigator: James J. Chou, Ph.D., Harvard University Medical School

New York Consortium on Membrane Protein Structure
Principal investigator: Wayne A. Hendrickson, Ph.D., New York Structural Biology Center

Transcontinental EM Initiative for Membrane Protein Structure
Principal investigator: David L. Stokes, Ph.D., New York Structural Biology Center

Transmembrane Protein Center
Principal investigator: Brian G. Fox, Ph.D., University of Wisconsin-Madison

Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions
Principal investigators: Robert Liddington, Ph.D., Burnham Institute for Medical Research; William James Nelson, Ph.D., Stanford University

Atoms-to-Animals: Structural Genomics of Immunity
Principal investigator: Stanley G. Nathenson, M.D., Albert Einstein College of Medicine of Yeshiva University

Chaperone-Enabled Studies of Epigenetic Regulation Enzymes
Principal investigator: Anthony A. Kossiakoff, Ph.D., University of Chicago

Consortia for High-Throughput-Enabled Structural Biology Partnerships
Principal investigator: Joshua N. Adkins, Ph.D., Battelle Pacific Northwest Laboratories

Partnership for High-Throughput-Enabled Biology of the Mitochondrial Proteome
Principal investigator: John L. Markley, Ph.D., University of Wisconsin-Madison

Ribonucleoprotein Complexes Regulating T-Cell Activation
Principal investigators: James R. Williamson, Ph.D., Scripps Research Institute; Daniel R. Salomon, M.D., Scripps Research Institute

Structure, Dynamics and Activation Mechanisms of Chemokine Receptors
Principal investigators: Tracy M. Handel, Ph.D., University of California, San Diego; Ruben A. Abagyan, Ph.D., University of California, San Diego

Structure-Function Studies of Tight Junction Membrane Proteins
Principal investigator: Alan S. Yu, M.D., University of Southern California

Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
Principal investigator: James C. Sacchettini, Ph.D., Texas A&M University

Structures of Protein Complexes Regulating Transcription in Embryonic Stem Cells
Principal investigator: Robert J. Fletterick, Ph.D., University of California, San Francisco

Materials Repository
Principal investigator: Josh Labaer, Ph.D., Arizona State University

Structural Biology Knowledgebase
Principal investigator:: Helen Berman, Ph.D., Rutgers University

There seems to be a live webcast from the ICCBM13, the 13th International Conference on the Crystallization of Biological Macromolecules at Trinity College in Dublin, Ireland. Stay tuned from 12th to the 16th September 2010 to learn what's new in protein crystallization science.

I'm not planning on staying up late over here on the west coast of the US. But the talks should be avalable for download at a later time, wouldn't you think so?

Cheers,

Peter

The quickest way to find the crystallization condition for a particular protein?

This: BMCD4 .

The Biomolecular Crystallization Database, now in its fourth version (4.02) and supporting better database query features than ever before is the best way to search for crystallization conditions for a particular protein.

You're starting a new protein crystallization project? Working on a protein that's been crystallized before? BMCD4 may give you a head start in successfully establishing crystallization. 

Just 5 min spent searching the BMCD4 may save you a month's worth of work in the crystallization lab.

Cheers,

Peter