Narrow Results

In this paper we present a scenario for the grid immersion of the procedures that solve the protein structural similarity determination problem. The emphasis is on the way various computational components and data resources are tied together into a workflow to be executed on a grid. The grid deployment has been organized according to the bag-of-service model: a set of different modules (with their data set) is made available to the application designers. Each module deals with a specific subproblem using a proper protein data representation. At the design level, the process of task selection produces a first general workflow that establishes which subproblems need to be solved and their temporal relations. A further refinement requires to select a procedure for each previously identified task that solves it: the choice is made among different available methods and representations. The final outcome is an instance of the workflow ready for execution on a grid. Our approach to protein structure comparison is based on a combination of indexing and dynamic programming techniques to achieve fast and reliable matching. All the components have been implemented on a grid infrastructure using Globus, and the overall tool has been tested by choosing proteins from different fold classes. The obtained results are compared against SCOP, a standard tool for the classification of known proteins.

CROs: Challenges to Contiuing Growth.

Life Sciences Capital Investing and Bioentrepreneurship in China and Asia Taking Off.

Flexing the Muscles of BioVentures in Japan and Beyond.

Future Directions and Growth of Biotechnology in China: An Analysis.

Potential Abounds, Biotechnology Research in China.

Biotechnology Parks: China into the Next Future.

Interview with Kurt Wüthrich – Why Structural Biology Matters.

The PCR Revolution – An Interview with Carl T Wittwer.

Vietnam Healthcare – The Next Growth Frontier?

Open Innovation: Next Frontier In Global Biopharma Industry.

INDIA – Zinc Treatment for Infections in Children.

JAPAN – Japan Pharma Portfolio Finds Renewed Strength through Record Growth in 2012.

JAPAN – Joint Development of a Novel Lyophilized Dual Chamber Prefillable Syringe System.

JAPAN – A Genetic Alternative to Fertilizer.

SINGAPORE – Made-in-Singapore H5N1 Bird Flu Diagnostic Kit - Detects All Known Strains of H5N1 Virus with a Single Test.

THAILAND – KEEEN, Thai Bioremediation Product, Awarded Gold Medal for "Bioremediation Agent developed to Greenovation Product".

EUROPE – MorphoSys Antibody Reaches Major Milestone in Collaboration with Roche.

EUROPE – New Technique to Predict Heart Attacks.

USA – FEI Launches 'Living Lab' for Structural Biology Research at NIH.

USA – Synthetic Platelets Built to Treat Bleeding.

USA – Software Scans Tongue for Signs of Disease.

USA – US Legislation Will Ensure Tighter Checks on Foreign Drug Factories.

Accelerator-based X-ray sources have contributed uniquely to the physical, engineering and life sciences. There has been a constant development of the sources themselves as well as of the necessary X-ray optics and detectors. These advances have combined to push X-ray science to the forefront in structural studies, achieving atomic resolution for complex protein molecules, to meV scale dynamics addressing problems ranging from geoscience to high-temperature superconductors, and to spatial resolutions approaching 10nm for elemental mapping as well as three-dimensional structures. Here we discuss accelerator-based photon science in the frame of imaging and highlight the importance of optics, detectors and computation/data science as well as the source technology. We look to a bright future for X-ray systems, integrating all components from accelerator sources to digital image production algorithms, and highlight aspects that make them unique scientific tools.

CRISPR-Cas9 is a revolutionary genome-editing tool. Understanding how Cas9 recognizes DNA and how to control its function will be critical in improving the system. We used single-molecule FRET to elucidate a key validation step during DNA target recognition. We also used X-ray crystallography to show how a Cas9 inhibitor is able to permit DNA binding but prevent cleavage. Finally, CRISPR research is notable not just for the exciting applications, but also for its profound ethical implications.

Accelerator-based X-ray sources have contributed uniquely to the physical, engineering and life sciences. There has been a constant development of the sources themselves as well as of the necessary X-ray optics and detectors. These advances have combined to push X-ray science to the forefront in structural studies, achieving atomic resolution for complex protein molecules, to meV scale dynamics addressing problems ranging from geoscience to high-temperature superconductors, and to spatial resolutions approaching 10nm for elemental mapping as well as three-dimensional structures. Here we discuss accelerator-based photon science in the frame of imaging and highlight the importance of optics, detectors and computation/data science as well as the source technology. We look to a bright future for X-ray systems, integrating all components from accelerator sources to digital image production algorithms, and highlight aspects that make them unique scientific tools.

There is significant interest in developing machine learning methods to model protein-ligand interactions but a scarcity of experimentally resolved protein-ligand structures to learn from. Protein self-contacts are a much larger source of structural data that could be leveraged, but currently it is not well understood how this data source differs from the target domain. Here, we characterize the 3D geometric patterns of protein self-contacts as probability distributions. We then present a flexible statistical framework to assess the transferability of these patterns to protein-ligand contacts. We observe that the level of transferability from protein self-contacts to protein-ligand contacts depends on contact type, with many contact types exhibiting high transferability. We then demonstrate the potential of leveraging information from these geometric patterns to aid in ligand pose-selection problems in protein-ligand docking. We publicly release our extracted data on geometric interaction patterns to enable further exploration of this problem.

Crystallization is recognized among structural biologists as a necessary process before three-dimensional structure can be solved at an atomic level. Crystallization has a dose of mysticism among protein chemist. Some treats it as an “art” and others as “black magic”. These concepts aroused from a limited knowledge in the physical chemistry of proteins in solution. Crystallization appears only in a metastable state. To define crystallization conditions the experiments are guided either by a chance search or by dedicated factorial design. Here we will briefly describe a factorial design method to rationally approach the metastable state. In summary, there is nothing mysterious in crystallization of biological macromolecules, and the success can often be achieved within a limited number of experiments.

CRISPR-Cas9 is a revolutionary genome-editing tool. Understanding how Cas9 recognizes DNA and how to control its function will be critical in improving the system. We used single-molecule FRET to elucidate a key validation step during DNA target recognition. We also used X-ray crystallography to show how a Cas9 inhibitor is able to permit DNA binding but prevent cleavage. Finally, CRISPR research is notable not just for the exciting applications, but also for its profound ethical implications.