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1.  Bis{(Z)-[(E)-2-(pyridin-2-yl­methyl­idene)hydrazin-1-yl­idene][(pyridin-2-yl)methyl­sulfan­yl]methane­thiol­ato}nickel(II) 
The title compound, [Ni(C13H11N4S2)2], was obtained by the reaction of S-2-picolyldi­thio­carbazate and pyridine-2-carbaldehyde with nickel(II) acetate. The NiII atom is located on a twofold rotation axis and is bonded to four N atoms at distances of 2.037 (8) and 2.109 (9) Å, and to two S atoms at a distance of 2.406 (3) Å, leading to a distorted octa­hedral coordination. The angle between the mean planes of the coordinating moieties of the two symmetry-related tridentate ligands is 83.3 (2)°. In the crystal, complex mol­ecules are linked by weak C—H⋯S hydrogen bonds, π–π inter­actions between the pyridine rings [centroid–centroid distance = 3.775 (9) Å] and C—H⋯π inter­actions. The hydrogen-bonding inter­actions lead to the formation of layers parallel to (010); π–π inter­actions link these layers into a three-dimensional network.
doi:10.1107/S1600536813013032
PMCID: PMC3684885  PMID: 23794987
2.  Analysis Tool Web Services from the EMBL-EBI 
Nucleic Acids Research  2013;41(Web Server issue):W597-W600.
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.
doi:10.1093/nar/gkt376
PMCID: PMC3692137  PMID: 23671338
3.  PSI-Search: iterative HOE-reduced profile SSEARCH searching 
Bioinformatics  2012;28(12):1650-1651.
Summary: Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains—homologous over-extension (HOE). PSI-Search combines an optimal Smith–Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2- for 4-fold fewer false-positives than JackHMMER, but is ~5% less sensitive.
Availability and implementation: PSI-Search is available from the authors as a standalone implementation written in Perl for Linux-compatible platforms. It is also available through a web interface (www.ebi.ac.uk/Tools/sss/psisearch) and SOAP and REST Web Services (www.ebi.ac.uk/Tools/webservices).
Contact: pearson@virginia.edu; rodrigo.lopez@ebi.ac.uk
doi:10.1093/bioinformatics/bts240
PMCID: PMC3371869  PMID: 22539666
4.  Watch out for Wii shoulder 
BMJ : British Medical Journal  2008;336(7636):110.
doi:10.1136/bmj.39461.631181.BE
PMCID: PMC2206259  PMID: 18202041
5.  (3R,4R,5R)-5-(Acetamido­meth­yl)-N-benzyl-3,4-dihy­droxy­tetra­hydro­furan-3-carboxamide 
X-ray crystallographic analysis with Cu Kα radiation established the relative configurations of the stereogenic centers in the title compound, C15H20N2O5, and clarified mechanistic ambiguities in the synthesis. The conformation of the five-membered ring approximates twisted, about a C—O bond. The absolute configuration of this carbon-branched dipeptide isostere was known based on the use of d-ribose as the starting material. Refinement of the Flack parameter gave an ambiguous result but the refined Hooft parameter is in agreement with the assumed (d-ribose) absolute structure. The crystal structure consists of N—H⋯O and O—H⋯O hydrogen-bonded bi-layers, with the terminal methyl and phenyl groups forming a hydro­phobic inter-layer inter­face. Some weak C—H⋯O inter­actions are also present.
doi:10.1107/S1600536810039589
PMCID: PMC3009327  PMID: 21588955
6.  4-Methoxy­phenyl 2,3,4,6-tetra-O-acetyl-1-thio-α-d-mannopyran­oside 
The title compound, C21H26O10S, was synthesized in a single step from mannose penta­acetate. The mol­ecular structure confirms the α configuration of the anomeric thioaryl substituent. Spectroscopic and melting-point data obtained for the title compound are in disagreement with those previously reported, indicating the previously reported synthesis [Durette & Shen (1980 ▶). Carbohydr. Res. 81, 261–274] to be erroneous. The crystal structure is stabilized by weak inter­molecular C—H⋯O hydrogen bonds.
doi:10.1107/S1600536808019338
PMCID: PMC2962034  PMID: 21203121
7.  (S)-3-Dimethyl­amino-2-{(4S,5R)-5-[(R)-2,2-dimethyl-1,3-dioxolan-4-yl]-2,2-dimethyl-1,3-dioxolan-4-yl}-2-hydroxy­propanoic acid 
The Kiliani reaction on 1-de­oxy-(N,N-dimethyl­amino)-d-fructose, itself readily available from reaction of dimethyl­amine and d-glucose, proceeded to give access to the title β-sugar amino acid, C15H27NO7. X-ray crystallography determined the stereochemistry at the newly formed chiral center. There are two mol­ecules in the asymmetric unit; they are related by a pseudo-twofold rotation axis and have very similar geometries, differing only in the conformation of one of the acetonide rings. All the acetonide rings adopt envelope conformations; the flap atom is oxygen in three of the rings, but carbon in one of them. There are two strong hydrogen bonds between the two independent mol­ecules, and further weak hydrogen bonds link the mol­ecules to form infinite chains running parallel to the a axis.
doi:10.1107/S1600536807066676
PMCID: PMC2915345  PMID: 21200859
8.  2,3,4,6-Tetra-O-benzoyl-4-nitro­phenyl-1-thio-α-d-mannopyran­oside–dichloro­methane–diethyl ether mixed solvate (1/0.53/0.38) 
The title compound, C40H31NO11S·0.53CH2Cl2·0.38C4H10O, was synthesized in two steps from mannose penta­acetate and single crystals were grown by slow evaporation. The structure was determined by single-crystal X-ray diffraction, confirming the α-configuration of the anomeric thioaryl substituent. The asymmetric unit contains two crystallographically distinct mol­ecules of the carbohydrate. The central pyran­ose rings of these are geometrically similar, but there are differences in the orientations of the benzoate substituents.
doi:10.1107/S1600536807064951
PMCID: PMC2915296  PMID: 21200803

Results 1-8 (8)