An enhanced version of comparative binding energy (COMBINE) analysis, named COMBINEr, based on both ligand-based and structure-based alignments has been used to build several 3-D QSAR models for the eleven human zinc-based histone deacetylases (HDACs). When faced with an abundance of data from diverse structure-activity sources, choosing the best paradigm for an integrative analysis is difficul...

This paper introduces the Tuple Graph (TuG) synopses, a new class of data summaries that enable accurate selectivity estimates for complex relational queries. The proposed summarization framework adopts a “semi-structured” view of the relational database, modeling a relational data set as a graph of tuples and join queries as graph traversals respectively. The key idea is to approximate the str...

PDZ domains have long been thought to cluster into discrete functional classes defined by their peptide-binding preferences. We used protein microarrays and quantitative fluorescence polarization to characterize the binding selectivity of 157 mouse PDZ domains with respect to 217 genome-encoded peptides. We then trained a multidomain selectivity model to predict PDZ domain-peptide interactions ...

This chapter describes a comprehensive computational study on the template-assisted and Pd(OAc)2-catalyzed meta-selective C–H olefination reaction. The reaction mechanism, the active form of catalyst, the potential role of silver salt and the origin of meta-selectivity were investigated in this work. The computational results demonstrated that the conventionally proposed monomeric Pd(OAc)2 mode...

In this paper we address the problem of optimizing the evaluation of boolean expressions in the context of object-oriented data modelling. We develop a new heuristic for optimizing the evaluation sequence of boolean expressions based on selectivity and cost estimates of the terms constituting the boolean expression. The quality and e ciency of the heuristic is evaluated based on a quantitative ...

This chapter describes a comprehensive computational study on the template-assisted and Pd(OAc)2-catalyzed meta-selective C–H olefination reaction. The reaction mechanism, the active form of catalyst, the potential role of silver salt and the origin of meta-selectivity were investigated in this work. The computational results demonstrated that the conventionally proposed monomeric Pd(OAc)2 mode...

This chapter describes a comprehensive computational study on the template-assisted and Pd(OAc)2-catalyzed meta-selective C–H olefination reaction. The reaction mechanism, the active form of catalyst, the potential role of silver salt and the origin of meta-selectivity were investigated in this work. The computational results demonstrated that the conventionally proposed monomeric Pd(OAc)2 mode...

The identification of the chemical structure of an odorant by the vertebrate olfactory system is thought to occur through the combinatorial activity from multiple receptors, each tuned to recognize different chemical features. What are the molecular determinants underlying the selectivity of individual odorant receptors for their cognate ligands? To address this question, we performed molecular...

Speech recognition in the human brain depends on spectral analysis coupled with temporal integration of auditory information. In primates, these processes are mirrored as selective responsiveness of neurons to speciesspecific vocalizations. Here, we used computational modeling of cortical neural networks to investigate how they achieve selectivity to speech stimuli. Stimulus material comprised ...

Self-organizing artificial neural networks are a popular tool for studying visual system development, in particular the cortical feature maps present in real systems that represent properties such as ocular dominance (OD), orientation-selectivity (OR) and direction selectivity (DS). They are also potentially useful in artificial systems, for example robotics, where the ability to extract and le...