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Abstract Computational modeling of protein–DNA complex structures has important implications in biomedical applications such as structure‐based, computer aided drug design. A key step in developing methods for accurate modeling of protein–DNA complexes is similarity assessment between models and their reference complex structures. Existing methods primarily rely on distance‐based metrics and generally do not consider important functional features of the complexes, such as interface hydrogen bonds that are critical to specific protein–DNA interactions. Here, we present a new scoring function, ComparePD, which takes interface hydrogen bond energy and strength into account besides the distance‐based metrics for accurate similarity measure of protein–DNA complexes. ComparePD was tested on two datasets of computational models of protein–DNA complexes generated using docking (classified as easy, intermediate, and difficult cases) and homology modeling methods. The results were compared with PDDockQ, a modified version of DockQ tailored for protein–DNA complexes, as well as the metrics employed by the community‐wide experiment CAPRI (Critical Assessment of PRedicted Interactions). We demonstrated that ComparePD provides an improved similarity measure over PDDockQ and the CAPRI classification method by considering both conformational similarity and functional importance of the complex interface. ComparePD identified more meaningful models as compared to PDDockQ for all the cases having different top models between ComparePD and PDDockQ except for one intermediate docking case.
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Evaluating Quantitative Measures for Assessing Functional Similarity in Engineering Design
Abstract The development of example-based design support tools, such as those used for design-by-analogy, relies heavily on the computation of similarity between designs. Various vector- and graph-based similarity measures operationalize different principles to assess the similarity of designs. Despite the availability of various types of similarity measures and the widespread adoption of some, these measures have not been tested for cross-measure agreement, especially in a design context. In this paper, several vector- and graph-based similarity measures are tested across two datasets of functional models of products to explore the ways in which they find functionally similar designs. The results show that the network-based measures fundamentally operationalize functional similarity in a different way than vector-based measures. Based upon the findings, we recommend a graph-based similarity measure such as NetSimile in the early stages of design when divergence is desirable and a vector-based measure such as cosine similarity in a period of convergence, when the scope of the desired function implementation is clearer.
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- Award ID(s):
- 2034448
- PAR ID:
- 10567499
- Publisher / Repository:
- ASME
- Date Published:
- Journal Name:
- Journal of Mechanical Design
- Volume:
- 144
- Issue:
- 3
- ISSN:
- 1050-0472
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Quantifying the association between components of multivariate random curves is of general interest and is a ubiquitous and basic problem that can be addressed with functional data analysis. An important application is the problem of assessing functional connectivity based on functional magnetic resonance imaging (fMRI), where one aims to determine the similarity of fMRI time courses that are recorded on anatomically separated brain regions. In the functional brain connectivity literature, the static temporal Pearson correlation has been the prevailing measure for functional connectivity. However, recent research has revealed temporally changing patterns of functional connectivity, leading to the study of dynamic functional connectivity. This motivates new similarity measures for pairs of random curves that reflect the dynamic features of functional similarity. Specifically, we introduce gradient synchronization measures in a general setting. These similarity measures are based on the concordance and discordance of the gradients between paired smooth random functions. Asymptotic normality of the proposed estimates is obtained under regularity conditions. We illustrate the proposed synchronization measures via simulations and an application to resting-state fMRI signals from the Alzheimer’s Disease Neuroimaging Initiative and they are found to improve discrimination between subjects with different disease status.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1115/1.4052302
