The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pKa values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional 1H and 13C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.
State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user- and software-dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure-based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord.
We describe a term infant with congenital cutaneous candidiasis (CCC), and review all cases in the English literature that reported birth weight and outcome. Presence of an intrauterine foreign body was a predisposing factor for development of CCC and subsequent preterm birth. The most common presentation of CCC in neonates weighing >1000 g was a generalized eruption of erythematous macules, papules, and/or pustules that sometimes evolved to include vesicles and bullae. Extremely low birth weight, premature neonates weighing <1000 g most often presented with a widespread desquamating and/or erosive dermatitis (10 of 15 [67%]), and were at greater risk for systemic infection with Candida spp (10 of 15 [67%]) and death (6 of 15 [40%] than those weighing >1000 g (5 of 48 [10%]; 4 of 48 [8%], respectively). Systemic antifungal therapy is recommended for neonates with burn-like dermatitis attributable to Candida spp, or positive blood, urine, and/or cerebrospinal fluid cultures. Systemic treatment also should be considered for all infants with CCC who have respiratory distress in the immediate neonatal period and/or laboratory signs of sepsis such as an elevated leukocyte count with an increase in immature forms or persistent hyperglycemia and glycosuria.
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