We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian-space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop-closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low energy model is selected. The CASP10 experiment suggests RosettaCM yields models with more accurate sidechain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%.

Memory for visually presented items is impaired by speech that is played as an irrelevant background. The paper presents the view that changing state of the auditory material is an important prerequisite for this disruption. Four experiments studied the effects of sounds varying in complexity in an attempt to establish which features of changing state in the auditory signal lead to diminished recall. Simple unvarying or repetitive speech sounds were not sufficient to induce the irrelevant speech effect (Experiment 1): in addition, simple analogues of speech, possessing regular or irregular envelopes and using a range of carriers, failed to imitate the action of speech (Experiment 2). Variability of between-utterance phonology in the irrelevant stream (Experiment 3) emerged as a crucial factor. Moreover, predictability of the syllable sequence did not reduce the degree of disruption (Experiment 4) suggesting that supra-syllabic characteristics of the speech are of little importance. The results broadly support the idea that disruption of short-term memory only occurs when the speech stream changes in state. It is argued that disruption occurs in memory when cues to serial order based on phonological representations of heard material interfere with the phonological codes of visual origin. It is suggested that cues to changing state of the speech input contaminate those associated with items of visual origin, which are already in a phonological store.

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