261 research outputs found
Pressure-dependent 13C chemical shifts in proteins: Origins and applications
Pressure-dependent (13)C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH(3), CH(2) and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the gamma-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual (13)C alpha shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas (13)C beta shifts retain significant dependence on local compression, making them less useful as structural restraints
Scaffold searching: automated identification of similar ring systems for the design of combinatorial libraries
Rigid ring systems can be used to position receptor-binding functional groups in 3D space and they thus play an increasingly important role in the design of combinatorial libraries. This paper discusses the use of shape-similarity methods to identify ring systems that are structurally similar to, and aligned with, a user-defined target ring system. These systems can be used as alternative scaffolds for the construction of a combinatorial library
Exploring the extent to which fluctuations in iceârafted debris reflect mass changes in the source ice sheet : a modelâobservation comparison using the last BritishâIrish Ice Sheet
The British and Irish Ice Sheet (BIIS) was highly dynamic during the Late Quaternary, with considerable regional differences in the timing and extent of its change. This was reflected in equally variable offshore iceârafted debris (IRD) records. Here we reconcile these two records using the FRUGAL intermediate complexity icebergâclimate model, with varying BIIS catchmentâlevel iceberg fluxes, to simulate change in IRD origin and magnitude along the western European margin at 1000âyear time steps during the height of the last BIIS glaciation (31â6âkaâbp). This modelled IRD variability is compared with existing IRD records from the deep ocean at five cores along this margin. There is general agreement of the temporal and spatial IRD variability between observations and model through this period. The Porcupine Bank off northwestern Ireland was confirmed by the modelling as a major dividing line between sites possessing exclusively northern or southern source regions for offshore IRD. During Heinrich events 1 and 2, the cores show evidence of a proportion of North American IRD, more particularly to the south of the British Isles. Modelling supports this southern bias for likely Heinrich impact, but also suggests North American IRD will only reach the British margin in unusual circumstances
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
This paper reports a detailed comparison of a range of different types of 2D fingerprints when used for similarity-based virtual screening with multiple reference structures. Experiments with the MDL Drug Data Report database demonstrate the effectiveness of fingerprints that encode circular substructure descriptors generated using the Morgan algorithm. These fingerprints are notably more effective than fingerprints based on a fragment dictionary, on hashing and on topological pharmacophores. The combination of these fingerprints with data fusion based on similarity scores provides both an effective and an efficient approach to virtual screening in lead-discovery programmes
D* Production in Deep Inelastic Scattering at HERA
This paper presents measurements of D^{*\pm} production in deep inelastic
scattering from collisions between 27.5 GeV positrons and 820 GeV protons. The
data have been taken with the ZEUS detector at HERA. The decay channel
(+ c.c.) has been used in the study. The
cross section for inclusive D^{*\pm} production with
and is 5.3 \pms 1.0 \pms 0.8 nb in the kinematic region
{ GeV and }. Differential cross
sections as functions of p_T(D^{*\pm}), and are
compared with next-to-leading order QCD calculations based on the photon-gluon
fusion production mechanism. After an extrapolation of the cross section to the
full kinematic region in p_T(D^{*\pm}) and (D^{*\pm}), the charm
contribution to the proton structure function is
determined for Bjorken between 2 10 and 5 10.Comment: 17 pages including 4 figure
Observation of Scaling Violations in Scaled Momentum Distributions at HERA
Charged particle production has been measured in deep inelastic scattering
(DIS) events over a large range of and using the ZEUS detector. The
evolution of the scaled momentum, , with in the range 10 to 1280
, has been investigated in the current fragmentation region of the Breit
frame. The results show clear evidence, in a single experiment, for scaling
violations in scaled momenta as a function of .Comment: 21 pages including 4 figures, to be published in Physics Letters B.
Two references adde
Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV
Results are presented from a search for a W' boson using a dataset
corresponding to 5.0 inverse femtobarns of integrated luminosity collected
during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV.
The W' boson is modeled as a heavy W boson, but different scenarios for the
couplings to fermions are considered, involving both left-handed and
right-handed chiral projections of the fermions, as well as an arbitrary
mixture of the two. The search is performed in the decay channel W' to t b,
leading to a final state signature with a single lepton (e, mu), missing
transverse energy, and jets, at least one of which is tagged as a b-jet. A W'
boson that couples to fermions with the same coupling constant as the W, but to
the right-handed rather than left-handed chiral projections, is excluded for
masses below 1.85 TeV at the 95% confidence level. For the first time using LHC
data, constraints on the W' gauge coupling for a set of left- and right-handed
coupling combinations have been placed. These results represent a significant
improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe
Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV
A search for a Higgs boson decaying into two photons is described. The
analysis is performed using a dataset recorded by the CMS experiment at the LHC
from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an
integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross
section of the standard model Higgs boson decaying to two photons. The expected
exclusion limit at 95% confidence level is between 1.4 and 2.4 times the
standard model cross section in the mass range between 110 and 150 GeV. The
analysis of the data excludes, at 95% confidence level, the standard model
Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The
largest excess of events above the expected standard model background is
observed for a Higgs boson mass hypothesis of 124 GeV with a local significance
of 3.1 sigma. The global significance of observing an excess with a local
significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is
estimated to be 1.8 sigma. More data are required to ascertain the origin of
this excess.Comment: Submitted to Physics Letters
Measurement of the Lambda(b) cross section and the anti-Lambda(b) to Lambda(b) ratio with Lambda(b) to J/Psi Lambda decays in pp collisions at sqrt(s) = 7 TeV
The Lambda(b) differential production cross section and the cross section
ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum
pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7
TeV using data collected by the CMS experiment at the LHC. The measurements are
based on Lambda(b) decays reconstructed in the exclusive final state J/Psi
Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and
Lambda to proton pion, using a data sample corresponding to an integrated
luminosity of 1.9 inverse femtobarns. The product of the cross section times
the branching ratio for Lambda(b) to J/Psi Lambda versus pt(Lambda(b)) falls
faster than that of b mesons. The measured value of the cross section times the
branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06
+/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for
anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are
statistical and systematic, respectively.Comment: Submitted to Physics Letters
Search for new physics in events with opposite-sign leptons, jets, and missing transverse energy in pp collisions at sqrt(s) = 7 TeV
A search is presented for physics beyond the standard model (BSM) in final
states with a pair of opposite-sign isolated leptons accompanied by jets and
missing transverse energy. The search uses LHC data recorded at a
center-of-mass energy sqrt(s) = 7 TeV with the CMS detector, corresponding to
an integrated luminosity of approximately 5 inverse femtobarns. Two
complementary search strategies are employed. The first probes models with a
specific dilepton production mechanism that leads to a characteristic kinematic
edge in the dilepton mass distribution. The second strategy probes models of
dilepton production with heavy, colored objects that decay to final states
including invisible particles, leading to very large hadronic activity and
missing transverse energy. No evidence for an event yield in excess of the
standard model expectations is found. Upper limits on the BSM contributions to
the signal regions are deduced from the results, which are used to exclude a
region of the parameter space of the constrained minimal supersymmetric
extension of the standard model. Additional information related to detector
efficiencies and response is provided to allow testing specific models of BSM
physics not considered in this paper.Comment: Replaced with published version. Added journal reference and DO
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