polandstudy7
polandstudy7
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Many virus-encoded proteins have intrinsically disordered regions that lack a stable, folded three-dimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes, and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins and compared our findings with data from non-viral proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy, e.g., a mean 36 per cent gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to severe acute respiratory syndrome coronavirus 2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response. We show that disorder prediction methods perform differently for viral and non-viral proteins, and that an ensemble approach can yield more robust and accurate predictions.The crystal structure of the hydrated title salt, C22H48N4 4+·4Cl-·4H2O (C22H48N4 = H4 L = 3,14-diethyl-2,6,13,17-tetra-azoniatri-cyclo-[16.4.0.07,12]doco-sa-ne), has been determined using synchrotron radiation at 220 K. find protocol The structure determination reveals that protonation has occurred at all four amine N atoms. The asymmetric unit comprises one half of the macrocyclic cation (completed by crystallographic inversion symmetry), two chloride anions and two water mol-ecules. The macrocyclic ring of the tetra-cation adopts an exodentate (3,4,3,4)-D conformation. The crystal structure is stabilized by inter-molecular hydrogen bonds involving the macrocycle N-H groups and water O-H groups as donors, and the O atoms of the water mol-ecules and chloride anions as acceptors, giving rise to a three-dimensional network.The amine 8-4-[(6-phenyl-pyridin-3-yl)meth-yl]piperazin-1-yl-3,4-di-hydro-quinolin-2(1H)-one was crystallized as the hydro-chloride salt, 4-(2-oxo-1,2,3,4-tetra-hydro-quinolin-8-yl)-1-[(6-phenyl-pyridin-3-yl)meth-yl]piperazin-1-ium chloride, C25H27N4 +·Cl- (I·HCl). The conformation of the organic cation is half-moon in shape enclosing the chloride anion. The piperidine ring of the 3,4-di-hydro-quinolin-2(1H)-one moiety has a screw-boat conformation, while the piperazine ring has a chair conformation. In the biaryl group, the pyridine ring is inclined to the phenyl ring by 40.17 (7) and by 36.86 (8)° to the aromatic ring of the quinoline moiety. In the crystal, the cations are linked by pairwise N-H⋯O hydrogen bonds, forming inversion dimers enclosing an R 2 2(8) ring motif. The Cl- anion is linked to the cation by an N-H⋯Cl hydrogen bond. These units are linked by a series of C-H⋯O, C-H⋯N and C-H⋯Cl hydrogen bonds, forming layers lying parallel to the ab plane.The crystal structure of 1,3-di-thiane 1,1,3,3-tetra-oxide, C4H8O4S2, has been determined to examine the inter-molecular C-H⋯O hydrogen bonds in a small mol-ecule with highly polarized hydrogen atoms. The crystals are monoclinic, space group Pn, with a = 4.9472 (5), b = 9.9021 (10), c = 7.1002 (7) Å and β = 91.464 (3)° with Z = 2. The mol-ecules form two stacks parallel to the a axis with the molecules being one a translation distance from each other. This stacking involves axial hydrogen atoms on one mol-ecule and the axial oxygen atoms on the adjacent mol-ecule in the stack. None of these C-H⋯O contacts is particularly short (all are > 2.4 Å). The many C-H⋯O contacts between the two stacks involve at least one equatorial hydrogen or oxygen atom. Again, no unusually short contacts are found. The whole crystal structure basically consists of a complex network of C-H⋯O contacts with no single, linear C-H⋯O contacts, only contacts that involve two (bifurcated), and mostly three or four neighbors.In the title compound, C20H19N3O4, the dihedral angles between the central pyrazole ring and the pendant phenyl and substituted benzene rings are 50.95 (8) and 3.25 (12)°, respectively, and an intra-molecular C-H⋯O link generates an S(6) ring. The benzodioxolyl ring adopts a shallow envelope conformation with the methyl-ene C atom as the flap. In the crystal, the mol-ecules are linked by non-classical C-H⋯O inter-actions, which generate a three-dimensional network. Solvent-accessible voids run down the c-axis direction and the residual electron density in these voids was modelled during the refinement process using the SQUEEZE algorithm [Spek (2015 ▸). Acta Cryst. C71, 9-18] within the structural checking program PLATON.In the title compound, C28H21N3O, the 1,2-di-hydro-pyridine ring of the 1,2,7,8-tetra-hydro-iso-quinoline ring system is planar as expected, while the cyclo-hexa-1,3-diene ring has a twist-boat conformation, with Cremer-Pople parameters Q T = 0.367 (2) A, θ = 117.3 (3)° and φ = 327.3 (4)°. The dihedral angles between the best planes through the iso-quinoline ring system and the three phenyl rings are 81.69 (12), 82.45 (11) and 47.36 (10)°. In the crystal, mol-ecules are linked via N-H⋯O and C-H⋯N hydrogen bonds, forming a three-dimensional network. Furthermore, the crystal packing is dominated by C-H⋯π bonds with a strong inter-action involving the phenyl H atoms. The role of the inter-molecular inter-actions in the crystal packing was clarified using Hirshfeld surface analysis, and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (46.0%), C⋯H/H⋯C (35.1%) and N⋯H/H⋯N (10.5%) contacts.

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