54,419 research outputs found
Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis
Aim: Molecular dynamics simulations and normal mode analysis are
well-established approaches to generate receptor conformational ensembles
(RCEs) for ligand docking and virtual screening. Here, we report new fast
molecular dynamics-based and normal mode analysis-based protocols combined with
conformational pocket classifications to efficiently generate RCEs. Materials
\& methods: We assessed our protocols on two well-characterized protein targets
showing local active site flexibility, dihydrofolate reductase and large
collective movements, CDK2. The performance of the RCEs was validated by
distinguishing known ligands of dihydrofolate reductase and CDK2 among a
dataset of diverse chemical decoys. Results \& discussion: Our results show
that different simulation protocols can be efficient for generation of RCEs
depending on different kind of protein flexibility
Classification of Time-Series Images Using Deep Convolutional Neural Networks
Convolutional Neural Networks (CNN) has achieved a great success in image
recognition task by automatically learning a hierarchical feature
representation from raw data. While the majority of Time-Series Classification
(TSC) literature is focused on 1D signals, this paper uses Recurrence Plots
(RP) to transform time-series into 2D texture images and then take advantage of
the deep CNN classifier. Image representation of time-series introduces
different feature types that are not available for 1D signals, and therefore
TSC can be treated as texture image recognition task. CNN model also allows
learning different levels of representations together with a classifier,
jointly and automatically. Therefore, using RP and CNN in a unified framework
is expected to boost the recognition rate of TSC. Experimental results on the
UCR time-series classification archive demonstrate competitive accuracy of the
proposed approach, compared not only to the existing deep architectures, but
also to the state-of-the art TSC algorithms.Comment: The 10th International Conference on Machine Vision (ICMV 2017
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Combinatorial optimization and metaheuristics
Today, combinatorial optimization is one of the youngest and most active areas of discrete mathematics. It is a branch of optimization in applied mathematics and computer science, related to operational research, algorithm theory and computational complexity theory. It sits at the intersection of several fields, including artificial intelligence, mathematics and software engineering. Its increasing interest arises for the fact that a large number of scientific and industrial problems can be formulated as abstract combinatorial optimization problems, through graphs and/or (integer) linear programs. Some of these problems have polynomial-time (“efficient”) algorithms, while most of them are NP-hard, i.e. it is not proved that they can be solved in polynomial-time. Mainly, it means that it is not possible to guarantee that an exact solution to the problem can be found and one has to settle for an approximate solution with known performance guarantees. Indeed, the goal of approximate methods is to find “quickly” (reasonable run-times), with “high” probability, provable “good” solutions (low error from the real optimal solution). In the last 20 years, a new kind of algorithm commonly called metaheuristics have emerged in this class, which basically try to combine heuristics in high level frameworks aimed at efficiently and effectively exploring the search space. This report briefly outlines the components, concepts, advantages and disadvantages of different metaheuristic approaches from a conceptual point of view, in order to analyze their similarities and differences. The two very significant forces of intensification and diversification, that mainly determine the behavior of a metaheuristic, will be pointed out. The report concludes by exploring the importance of hybridization and integration methods
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