Journal of Computational Chemistry

Cover image for Vol. 36 Issue 2

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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Recently Published Articles

  1. Search for the global minimum structures of AlB3H2n (n = 0 − 6) clusters

    İskender Muz, Osman Canko, Murat Atiş and Erdem Kamil Yıldırım

    Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23812

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    The global minimum structures of AlB3H2n (n = 0–6) clusters are investigated and the chemical bonding patterns of the most stable isomers are analyzed by the adaptive natural density partitioning method.

  2. New insights into the meaning and usefulness of principal component analysis of concatenated trajectories

    Gustavo Pierdominici-Sottile and Juliana Palma

    Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23811

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    Combined principal component analysis (combined-PCA) is a technique usually employed to analyze structural and dynamical differences between alternative conformations of a given protein. However, analytical formulas showing what is to be expected and what is not to be expected from a combined-PCA have never been provided. Here, we present and discuss such formulas. We believe that they will be useful to enlighten the discussions of the results of combined-PCA.

  3. STOCK: Structure mapper and online coarse-graining kit for molecular simulations

    Staš Bevc, Christoph Junghans and Matej Praprotnik

    Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23806

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    STOCK is a web-based toolkit for setting up coarse-grained molecular simulations. One can define a molecular mapping from high to low resolution with the aid of a molecular visualizer. Additionally, one may generate effective potentials for coarse-grained simulations preserving structural properties of the underlying higher resolution model. The tool is available at http://stock.cmm.ki.si

  4. k-Nearest neighbors optimization-based outlier removal

    Abraham Yosipof and Hanoch Senderowitz

    Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23803

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    A new iterative method for the identification and removal of outliers from quantitative structure activity relationship (QSAR) datasets is described. This method is based on a kNN optimization algorithm, and named kNN optimization-based outlier removal. The method is able to maintain the internal diversity of the parent dataset and at the same time produce QSAR models with better prediction statistics than other outlier removal methods.

  5. BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials

    Pablo M. De Biase, Suren Markosyan and Sergei Noskov

    Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23799

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    The transport of DNA and ions by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. BROMOC Suite is a software package designed to perform Brownian dynamics simulations up to several milliseconds long of large biological systems (BROMOC), to develop effective potentials for solute-ion interactions based on RDF from all-atom Molecular Dynamics (IMC-MACRO), and to do a wide variety of pre-processing and post-simulation analysis (BROMOC Tools).

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