Searching for authors named "Dimitris Agrafiotis" – sorted by Relevance.
12 documents found, showing 1 through 10.
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Stochastic algorithms for maximizing molecular diversity
- …A common problem in the emerging field of combinatorial drug design is the selection of an appropriate subset of compounds for chemical synthesis and biological evaluation. In this paper, we introduce a new family of selection algorithms that combine a stochastic search engine with a user-defined ob…
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On the Use of Information Theory for Assessing Molecular Diversity
- …In a recent article published in Molecules, Lin presented a novel approach for assessing molecular diversity based on Shannon’s information theory. In this method, a set of compounds is viewed as a static collection of microstates which can register information about their environment at some predet…
- Cited by 4 (3 self) – Add To MetaCart
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Constant time algorithm for estimating the diversity of large chemical libraries
- …We describe a novel diversity metric for use in the design of combinatorial chemistry and high-throughput screening experiments. The method estimates the cumulative probability distribution of intermolecular dissimilarities in the collection of interest and then measures the deviation of that distri…
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A geodesic framework for analyzing molecular similarities
- …A fast self-organizing algorithm for extracting the minimum number of independent variables that can fully describe a set of observations was recently described (Agrafiotis, D. K.; Xu, H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15869-15872). The method, called stochastic proximity embedding (SPE), a…
- Cited by 2 (1 self) – Add To MetaCart
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Nonlinear Mapping Networks
- …Among the many dimensionality reduction techniques that have appeared in the statistical literature, multidimensional scaling and nonlinear mapping are unique for their conceptual simplicity and ability to reproduce the topology and structure of the data space in a faithful and unbiased manner. Howe…
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Design and Prioritization of Plates for HighThroughput Screening
- …A general algorithm for the prioritization and selection of plates for high-throughput screening is presented. The method uses a simulated annealing algorithm to search through the space of plate combinations for the one that maximizes some user-defined objective function. The algorithm is robust an…
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Ultrafast algorithm for designing focused combinatorial arrays
- …A novel greedy algorithm for the design of focused combinatorial arrays is presented. The method is applicable when the objective function is decomposable to individual molecular contributions and makes use of a heuristic that allows the independent evaluation and ranking of candidate reagents in ea…
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Stochastic similarity selections from large combinatorial libraries
- …A stochastic procedure for similarity searching in large virtual combinatorial libraries is presented. The method avoids explicit enumeration and calculation of descriptors for every virtual compound, yet provides an optimal or nearly optimal similarity selection in a reasonable time frame. It is ba…
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Conformational Sampling by Self-Organization
- …A new stochastic algorithm for conformational sampling is described. The algorithm generates molecular conformations that are consistent with a set of geometric constraints, which include interatomic distance bounds and chiral volumes derived from the molecular connectivity table. The algorithm repe…
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Agrafiotis, “Nonlinear Mapping of Massive Data Sets by Fuzzy Clustering and Neural Networks
- …ABSTRACT: Producing good low-dimensional representations of high-dimensional data is a common and important task in many data mining applications. Two methods that have been particularly useful in this regard are multidimensional scaling and nonlinear mapping. These methods attempt to visualize a se…
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