Journal of Computational Chemistry
Copyright © 2014 Wiley Periodicals, Inc., A Wiley Company
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
Recently Published Articles
- 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
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.
- 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
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.
- 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
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
- k-Nearest neighbors optimization-based outlier removal
Abraham Yosipof and Hanoch Senderowitz
Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23803
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.
- 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
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).