312 research outputs found
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. Here, we present an online implementation of that alignment algorithm based on such probabilities. Our server takes as input a query RNA sequence and a large genome sequence, and outputs a list of hits that are above a mean posterior probability threshold. The output is presented in a format suited to local alignment. It can also be viewed within the PLAST alignment viewer applet that provides a list of all hits found and highlights regions of high posterior probability within each local alignment. The server is freely available at http://plastrna.njit.edu
How accurate and statistically robust are catalytic site predictions based on closeness centrality?
<p>Abstract</p> <p>Background</p> <p>We examine the accuracy of enzyme catalytic residue predictions from a network representation of protein structure. In this model, amino acid α-carbons specify vertices within a graph and edges connect vertices that are proximal in structure. Closeness centrality, which has shown promise in previous investigations, is used to identify important positions within the network. Closeness centrality, a global measure of network centrality, is calculated as the reciprocal of the average distance between vertex <it>i </it>and all other vertices.</p> <p>Results</p> <p>We benchmark the approach against 283 structurally unique proteins within the Catalytic Site Atlas. Our results, which are inline with previous investigations of smaller datasets, indicate closeness centrality predictions are statistically significant. However, unlike previous approaches, we specifically focus on residues with the very best scores. Over the top five closeness centrality scores, we observe an average true to false positive rate ratio of 6.8 to 1. As demonstrated previously, adding a solvent accessibility filter significantly improves predictive power; the average ratio is increased to 15.3 to 1. We also demonstrate (for the first time) that filtering the predictions by residue identity improves the results even more than accessibility filtering. Here, we simply eliminate residues with physiochemical properties unlikely to be compatible with catalytic requirements from consideration. Residue identity filtering improves the average true to false positive rate ratio to 26.3 to 1. Combining the two filters together has little affect on the results. Calculated p-values for the three prediction schemes range from 2.7E-9 to less than 8.8E-134. Finally, the sensitivity of the predictions to structure choice and slight perturbations is examined.</p> <p>Conclusion</p> <p>Our results resolutely confirm that closeness centrality is a viable prediction scheme whose predictions are statistically significant. Simple filtering schemes substantially improve the method's predicted power. Moreover, no clear effect on performance is observed when comparing ligated and unligated structures. Similarly, the CC prediction results are robust to slight structural perturbations from molecular dynamics simulation.</p
The Single-Particle Structure of Neutron-Rich Nuclei of Astrophysical Interest at the Ornl Hribf
The rapid nuetron-capture process (r process) produces roughly half of the
elements heavier than iron. The path and abundances produced are uncertain,
however, because of the lack of nuclear strucure information on important
neutron-rich nuclei. We are studying nuclei on or near the r-process path via
single-nucleon transfer reactions on neutron-rich radioactive beams at ORNL's
Holifield Radioactive Ion Beam Facility (HRIBF). Owing to the difficulties in
studying these reactions in inverse kinematics, a variety of experimental
approaches are being developed. We present the experimental methods and initial
results.Comment: Proceedings of the Third International Conference on Fission and
Properties of Neutron-Rich Nucle
Direct reaction measurements with a 132Sn radioactive ion beam
The (d,p) neutron transfer and (d,d) elastic scattering reactions were
measured in inverse kinematics using a radioactive ion beam of 132Sn at 630
MeV. The elastic scattering data were taken in a region where Rutherford
scattering dominated the reaction, and nuclear effects account for less than 8%
of the cross section. The magnitude of the nuclear effects was found to be
independent of the optical potential used, allowing the transfer data to be
normalized in a reliable manner. The neutron-transfer reaction populated a
previously unmeasured state at 1363 keV, which is most likely the
single-particle 3p1/2 state expected above the N=82 shell closure. The data
were analyzed using finite range adiabatic wave calculations and the results
compared with the previous analysis using the distorted wave Born
approximation. Angular distributions for the ground and first excited states
are consistent with the previous tentative spin and parity assignments.
Spectroscopic factors extracted from the differential cross sections are
similar to those found for the one neutron states beyond the benchmark
doubly-magic nucleus 208Pb.Comment: 22 pages, 7 figure
Fermi surface of the colossal magnetoresistance perovskite La_{0.7}Sr_{0.3}MnO_{3}
Materials that exhibit colossal magnetoresistance (CMR) are currently the
focus of an intense research effort, driven by the technological applications
that their sensitivity lends them to. Using the angular correlation of photons
from electron-positron annihilation, we present a first glimpse of the Fermi
surface of a material that exhibits CMR, supported by ``virtual crystal''
electronic structure calculations. The Fermi surface is shown to be
sufficiently cubic in nature that it is likely to support nesting.Comment: 5 pages, 5 PS figure
Spin Wave Theory of Double Exchange Ferromagnets
We construct the 1/S spin-wave expansion for double exchange ferromagnets at
T=0. It is assumed that the value of Hund's rule coupling, J_H, is sufficiently
large, resulting in a fully saturated, ferromagnetic half-metallic ground
state. We evaluate corrections to the magnon dispersion law, and we also find
that, in contrast to earlier statements in the literature, magnon-electron
scattering does give rise to spin wave damping. We analyse the momentum
dependence of these quantities and discuss the experimental implications for
colossal magnetoresistance compounds.Comment: 4 pages, Latex-Revtex, 2 PostScript figures. Minor revisions,
references added. See also cond-mat/990921
Orientation and symmetries of Alexandrov spaces with applications in positive curvature
We develop two new tools for use in Alexandrov geometry: a theory of ramified
orientable double covers and a particularly useful version of the Slice Theorem
for actions of compact Lie groups. These tools are applied to the
classification of compact, positively curved Alexandrov spaces with maximal
symmetry rank.Comment: 34 pages. Simplified proofs throughout and a new proof of the Slice
Theorem, correcting omissions in the previous versio
The magic nature of 132Sn explored through the single-particle states of 133Sn
Atomic nuclei have a shell structure where nuclei with 'magic numbers' of
neutrons and protons are analogous to the noble gases in atomic physics. Only
ten nuclei with the standard magic numbers of both neutrons and protons have so
far been observed. The nuclear shell model is founded on the precept that
neutrons and protons can move as independent particles in orbitals with
discrete quantum numbers, subject to a mean field generated by all the other
nucleons. Knowledge of the properties of single-particle states outside nuclear
shell closures in exotic nuclei is important for a fundamental understanding of
nuclear structure and nucleosynthesis (for example the r-process, which is
responsible for the production of about half of the heavy elements). However,
as a result of their short lifetimes, there is a paucity of knowledge about the
nature of single-particle states outside exotic doubly magic nuclei. Here we
measure the single-particle character of the levels in 133Sn that lie outside
the double shell closure present at the short-lived nucleus 132Sn. We use an
inverse kinematics technique that involves the transfer of a single nucleon to
the nucleus. The purity of the measured single-particle states clearly
illustrates the magic nature of 132Sn.Comment: 19 pages, 5 figures and 4 table
Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling
Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the integer body-bar Pebble Game (PG) algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations to accurately account for fluctuations in network topology. We have developed a mean field Virtual Pebble Game (VPG) that represents the ensemble of networks by a single effective network. That is, all possible number of distance constraints (or bars) that can form between a pair of rigid bodies is replaced by the average number. The resulting effective network is viewed as having weighted edges, where the weight of an edge quantifies its capacity to absorb degrees of freedom. The VPG is interpreted as a flow problem on this effective network, which eliminates the need to sample. Across a nonredundant dataset of 272 protein structures, we apply the VPG to proteins for the first time. Our results show numerically and visually that the rigidity characterizations of the VPG accurately reflect the ensemble averaged properties. This result positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability
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