For some interesting links to the international year of chemistry pages, directly go to the wonderful initiative CatQuimica.cat.

“QM and MM methods: Obtaining an atomic and electronic view of nature”, by Víctor Guallar, Friday April 1
Víctor Guallar, ICREA-Barcelona Supercomputing Center, will give a talk entitled “QM and MM methods: Obtaining an atomic and electronic view of nature” on Friday April 1 at 11:00h at the seminar room 473.10– PRBB. This talk is part of the Structural Biology Seminars.

Friday, April 1st 2011; 11:00-12:00
Room 473 (PRBB – 4th Floor)

We will present our recent method development to map electronic and atomic coordinates for complex biological processes. 1) The atomic detailed mechanism of long range conformational changes remains a great challenge. Many biologically relevant processes, involving large domain motions or quaternary rearrangement, occur in the millisecond time scale, out of the reach of Molecular Dynamic techniques. PELE (Protein Energy Landscape Exploration), combines protein structure prediction techniques with a metropolis algorithm and is capable of fast mapping the slow motion energy landscape. 2) Electron transfer is one of the simplest but crucial reactions in biochemistry present in almost. Mixed quantum mechanics molecular mechanics methods (QMMM) offer a valuable computational tool for understanding the electron transfer pathway in protein-substrate and protein-protein complexes. By selectively turning on/off different residues in the quantum region, we have developed a novel approach capable of obtaining the electron pathway for short and large range interactions.

Short CV

Past: PhD 1999 Autonomous University of Barcelona August 2000-August 2003, Postdoctoral Researcher, Columbia University Chemistry Department, New York City, NY (USA) August 2003- July 2006: Assistant Professor, Washington University in St. Louis, School of Medicine, Biochemistry & Molecular Biophysics (USA) Current: ICREA Professor, Life Science Department at the Barcelona Supercomputing Center and Adjunct Professor at Washington University in St. Louis (USA) Advice editor for Biophysical Chemistry, Elsevier Group.

Conference hosted by the CBBL:

Isabel Usón
Molecular Biology Institute of Barcelona (IBMB)

“Computational methods to solve the crystallographic phase problem”

Friday, March 25th 2011; 11:00-12:00
Seminar Xipre (PRBB) – 1st Floor, room 173.06

Given the phase problem, determining an initial model from the diffraction data (phasing) is a bottleneck in crystallography. Ab Initio phasing of macromolecular structures with no heavy atoms has been limited to cases with up to around 1000 atoms in the asymmetric unit, diffracting to atomic resolution. Both the size and resolution barriers have been overcome in the case of several previously unknown structures. Proteins with a few thousand atoms, diffracting to 2Å have been solved through a combination of location of model fragments such as poly-alanine alpha-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correctly positioned fragments, the method has to test many putative groups of fragments in parallel, thus calculations are performed in a grid. The method has been called after the Italian painter Arcimboldo, who used to compose portraits out of fruits and vegetables. In the case of our program, most collections of fragments remain a “still-life”, but some are correct enough for density modification to reveal the protein’s portrait. The same methodology can be used to build a protein out of shredded fragments from a low homology or NMR model where conventional molecular replacement has failed.

Short CV

Chemistry degree in 1987, University of Zaragoza, Dr. Rer. Nat. University of Zaragoza in 1992, Product Research Scientist at the European Research Center in Brussels with Procter & Gamble for 15 months. Moved for a HCM postdoc at the University of Göttingen (Germany) and stayed for an Habilitation (German Higher Doctorate) at (1996-2001) with Prof. Sheldrick, and as C2 leading an independent research group. Moved to Barcelona in September 2003 joining the IBMB-CSIC as ICREA Research Professor.

In a series of interesting views on how to make our accomplishments visible to other researchers and to produce impact in general with our research activities, Phillip E. Bourne has released a new article, this time on “Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia”. In his new article, Bourne points to obvious (a posteriori) rules that may be important to be considered for a position. Such type of ideas, which are alike the ideas one can obtain from, let’s say, a course on business plan writing, have become more and more relevant in a world that is continuously changing and where your name is practically nothing in the middle of such an amount of competing names bearing similar or most of the times better quality, knowledge or perspectives.

At the end of the paper, Bourne emphasizes what is more important to me: sell yourself, but do not OVERsell yourself. In research we can find too many examples of people pushing sometimes too much the boundaries of what is their real knowledge (however good this may be) into the world of easy media and overacting. The problem is that not so careful referees (either of an academic article or a press release) become too impressed with the flashes (or having met this guy in that particular conference) and forget about addressing the actual quality of the information being released.

Thanks to the efforts of Gianni de Fabritiis and Gian Gaetano Tartaglia, the PRBB will host a new series of Structural Biology seminars.

You will find an updated calendar at http://prbbstructure.wordpress.com/.