Journal of Computational Chemistry

Cover image for Vol. 37 Issue 5

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

Impact Factor: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

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

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  1. Additive CHARMM force field for naturally occurring modified ribonucleotides

    You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. MacKerell Jr. and Lennart Nilsson

    Article first published online: 3 FEB 2016 | DOI: 10.1002/jcc.24307

    Thumbnail image of graphical abstract

    All naturally occurring modified ribonucleotides were systematically parametrized in this additive CHARMM force field. This will allow for computational investigation of how specific modifications influence RNA structures, providing insight on structural stability and binding affinity of RNA complexes, such as transfer RNA participating in decoding interactions on the ribosome.

  2. Focused grid-based resampling for protein docking and mapping

    Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda and Dima Kozakov

    Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24273

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    The fast Fourier transform (FFT) algorithm enables extremely fast evaluation of energy functions, and hence has been used with great success for protein-protein docking and for the characterization of the binding properties of proteins by docking small probe molecules. While both applications of FFT involve global systematic sampling, the same algorithm can also be used to refine the results by focused resampling on the regions of interest using finer grids or by retaining more structures.

  3. Structures and energetics of complexation of metal ions with ammonia, water, and benzene: A computational study

    Bhaskar Sharma, Y. Indra Neela and G. Narahari Sastry

    Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24288

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    Understanding metal ions with amines, water and aromatic systems is of outstanding importance in biology. An exhaustive computational study has been carried out up to CCSD(T)/def2-TZVP level on a number of main group and transition metal ion interaction with benzene, water and ammonia. Density functional theory based symmetry adapted perturbation theory(DFT-SAPT) analysis has been performed to estimate the contribution of various energy components for the binding energy.

  4. The catalytic effect of the NH3 base on the chemical events in the caryolene-forming carbocation cascade

    Daniela E. Ortega, Quynh Nhu N. Nguyen, Dean J. Tantillo and Alejandro Toro-Labbé

    Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24294

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    Caryolene formation occurs asynchronously in a concerted way through carbocationic rearrangements involving the generation of a secondary or a tertiary carbocation, depending on the absence or in the presence of NH3. Both mechanisms are analyzed within the general framework of the reaction force. The reaction force constant is used to gain insights into the synchronicity of the mechanisms and the reaction electronic flux aids characterization of the electronic activity taking place during reaction.

  5. Fast search algorithms for computational protein design

    Seydou Traoré, Kyle E. Roberts, David Allouche, Bruce R. Donald, Isabelle André, Thomas Schiex and Sophie Barbe

    Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24290

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    Computational protein design (CPD) through Cost Function Networks (CFN) provides important speedups to explore large sequence-conformation spaces and provably identifies the sequence with the conformation of optimal stability (Global Minimum Energy Conformation, GMEC). In addition to quickly finding the GMEC of highly complex protein design problems, CFN-based methods also enable the efficient enumeration of suboptimal solutions. These approaches offer an attractive alternative to the usual CPD methods and were implemented in the well-established CPD package Osprey.

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