12 research outputs found
Modelling the nucleon wave function from soft and hard processes
Current light-cone wave functions for the nucleon are unsatisfactory since
they are in conflict with the data of the nucleon's Dirac form factor at large
momentum transfer. Therefore, we attempt a determination of a new wave function
respecting theoretical ideas on its parameterization and satisfying the
following constraints: It should provide a soft Feynman contribution to the
proton's form factor in agreement with data; it should be consistent with
current parameterizations of the valence quark distribution functions and
lastly it should provide an acceptable value for the \jp \to N \bar N decay
width. The latter process is calculated within the modified perturbative
approach to hard exclusive reactions. A simultaneous fit to the three sets of
data leads to a wave function whose -dependent part, the distribution
amplitude, shows the same type of asymmetry as those distribution amplitudes
constrained by QCD sum rules. The asymmetry is however much more moderate as in
those amplitudes. Our distribution amplitude resembles the asymptotic one in
shape but the position of the maximum is somewhat shifted.Comment: 32 pages RevTex + PS-file with 5 figures in uu-encoded, compressed
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Structure-Based Predictive Models for Allosteric Hot Spots
In allostery, a binding event at one site in a protein modulates the behavior of a distant site. Identifying residues that relay the signal between sites remains a challenge. We have developed predictive models using support-vector machines, a widely used machine-learning method. The training data set consisted of residues classified as either hotspots or non-hotspots based on experimental characterization of point mutations from a diverse set of allosteric proteins. Each residue had an associated set of calculated features. Two sets of features were used, one consisting of dynamical, structural, network, and informatic measures, and another of structural measures defined by Daily and Gray [1]. The resulting models performed well on an independent data set consisting of hotspots and non-hotspots from five allosteric proteins. For the independent data set, our top 10 models using Feature Set 1 recalled 68–81% of known hotspots, and among total hotspot predictions, 58–67% were actual hotspots. Hence, these models have precision P = 58–67% and recall R = 68–81%. The corresponding models for Feature Set 2 had P = 55–59% and R = 81–92%. We combined the features from each set that produced models with optimal predictive performance. The top 10 models using this hybrid feature set had R = 73–81% and P = 64–71%, the best overall performance of any of the sets of models. Our methods identified hotspots in structural regions of known allosteric significance. Moreover, our predicted hotspots form a network of contiguous residues in the interior of the structures, in agreement with previous work. In conclusion, we have developed models that discriminate between known allosteric hotspots and non-hotspots with high accuracy and sensitivity. Moreover, the pattern of predicted hotspots corresponds to known functional motifs implicated in allostery, and is consistent with previous work describing sparse networks of allosterically important residues