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We discuss the role that synchrotron light sources, such as SESAME, could play in improving the socioeconomic conditions in developing countries. After providing a brief description of a synchrotron light source, we discuss the important role that they played in the development of several economically emerging countries. Then we describe the state of synchrotron science in South Africa and that country’s leadership role in founding the African Light Source initiative. Next, we highlight a new initiative called Lightsources for Africa, the Americas & Middle East Project, which is a global initiative led by the International Union of Pure and Applied Physics and the International Union of Crystallography, with initial funding provided by the International Council for Science. Finally, we comment on a new technology called the multibend achromat that has launched a new paradigm for the design of synchrotron light sources that should be attractive for construction in developing countries.

SINGAPORE – Mitigating Disease Outbreaks with Smart Mapping Technology.

SINGAPORE – Nestlé Expands Research and Innovation Activities in Asia with New Research Centre in Singapore's Biopolis.

UNITED STATES – Cornell Researchers Report Blood-Brain Barrier Breakthrough.

UNITED STATES – Blueberries May Offer Benefits for Post-Traumatic Stress Disorder.

UNITED STATES – New Mouse Model to Aid Testing of Zika Vaccine, Therapeutics.

UNITED STATES – Harvard Scientists Report on Novel Method for Extending the Life of Implantable Devices in situ.

UNITED STATES & INDIA – Government Use of Technology Has Potential to Increase Food Security.

UNITED KINGDOM – OGT Develops New FISH Probes in ‘Outstanding’ Innovate UK Project.

UNITED KINGDOM – FEI Partners with Five Pharmaceutical Companies, the Medical Research Council and the University of Cambridge to Form Cryo-EM Research Consortium.

RUSSIA – Innovative Russian Medicine Mobilises Human Immune System to Fight Cancer.

AUSTRALIA – Positive Clinical Data from CAVATAK™ and YERVOY^® Combination Presented at the 2016 AACR Annual Meeting.

JAPAN – Bayer Receives Approval for Xofigo^® in Japan.

Many Poisson–Boltzmann equation (PBE) solvers have been developed to calculate electrostatic energy of biomolecules, and each PBE solver has its advantages. In this study two PBE solvers — DelPhi and PBSA module in AMBER — are compared in terms of calculation results, convergence and program-running time by calculating the electrostatic solvation energy for a test set composed of 4 Kirkwood models and another test set of 25 protein structures. The protein structures were pretreated by AMBER and AMBER99SB force field parameters were used in all calculations. It is found that (i) At fine grids, both PBE solvers can produce accurate results on test set 1 and consistent results with each other on test set 2, with differences between each other varying from several to ~ 10 kcal/mol. (ii) Under convergence criterion "absolute value of relative error is less than or equal to 2% (|RE| ≤ 2%)", both PBE solvers need very fine grids to produce convergent results on small and complex Kirkwood models, while grid spacings of ≤ 0.5 Å–0.6 Å are well enough for them to achieve good convergent results on various molecular structures. We recommend users to adopt such grid spacing in using of these PBE solvers so as to get good enough convergent results. (iii) In terms of time consumption, DelPhi appears to be more time-saving than PBSA. In summary, according to our comparison, DelPhi and PBSA are paralleled good PBE solvers. The convergence of PBSA is a little better than DelPhi, while DelPhi exceeds PBSA in running speed.

We propose new methods for finding similarities in protein structure databases. These methods extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. The feature vectors are then indexed using a multidimensional index structure. Our first technique considers the problem of finding proteins similar to a given query protein in a protein dataset. It quickly finds promising proteins using the index structure. These proteins are then aligned to the query protein using a popular pairwise alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Our second technique considers the problem of joining two protein datasets to find an all-to-all similarity. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times, while keeping the sensitivity similar. Our technique can also be incorporated with DALI and CE to improve their running times by a factor of 2 and 2.7 respectively. The software is available online at .

Voronoi tessellations and their dual Delaunay tetrahedral tessellations provide versatile representations of three-dimensional structures of proteins, allowing a strict definition of neighborhoods of the different amino acids, considered as rigid entities. They give geometrical and topological information coded in the adjacency matrix (often called contact map in biology). Using this approach, this paper presents a two-dimensional description of internal surfaces, which are tools used to understand the conformation of globular proteins. These surfaces are triangulated surfaces tiled by faces of Delaunay tetrahedra. Two simple types of surfaces are presented, characterized by their topology: disk-like or torus-like. The torus-like surface is relevant in the description of secondary structures. The disk-like surface characterizes the collapse of the chain onto itself.

Due to the large number of available protein structure alignment algorithms, a lot of effort has been made to define robust measures to evaluate their performances and the quality of generated alignments. Most quality measures involve the number of aligned residues and the RMSD. In this work, we analyze how these two properties are influenced by different residue assignment strategies as employed in common non-sequential structure alignment algorithms. Therefore, we implemented different residue assignment strategies into our non-sequential structure alignment algorithm GANGSTA+. We compared the resulting numbers of aligned residues and RMSDs for each residue assignment strategy and different alignment algorithms on a benchmark set of circular-permuted protein pairs. Unfortunately, differences in the residue assignment strategies are often ignored when comparing the performances of different algorithms. However, our results clearly show that this may strongly bias the observations. Bringing residue assignment strategies in line can explain observed performance differences between entirely different alignment algorithms. Our results suggest that performance comparison of non-sequential protein structure alignment algorithms should be based on the same residue assignment strategy.

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs.