Journal of Computational Chemistry

Cover image for Vol. 34 Issue 11

30 April 2013

Volume 34, Issue 11

Pages i–iv, 893–985

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 34, Issue 11 (pages i–ii)

      Version of Record online: 20 MAR 2013 | DOI: 10.1002/jcc.23289

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      The front cover illustrates the parallel molecular docking of large databases on the Sequoia, a petascale IBM Blue Gene/Q supercomputer at Lawrence Livermore National Laboratory. A mixed parallel scheme that combines MPI and multithreading is implemented by Xiaohua Zhang, Sergio E. Wong, and Felice C. Lightstone on page 915 in the Vina molecular docking program named VinaLC, where LC stands for Livermore Computing. Parallel performance analysis shows the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations take only 1.4 hours on about 15K CPUs. The picture shows ligands that have been docked into various receptors to form ligand-receptor complexes via calculations on the Sequoia.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 11 (pages iii–iv)

      Version of Record online: 20 MAR 2013 | DOI: 10.1002/jcc.23290

      Thumbnail image of graphical abstract

      TargetATPsite, a new method based on residue evolution image sparse representation and classifier ensemble is developed for predicting ATP-binding, sites from primary sequences, as presented by Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhen-Min Tang, and Jing-Yu Yang on page 974. The high performance of TargetATPsite originates from the good discriminative capability of the new image sparse representation feature and the power of the modified AdaBoost classifier ensemble. TargetATPsite also features the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes (pages 893–903)

      Jennifer L. Knight, Joseph D. Yesselman and Charles L. Brooks III

      Version of Record online: 7 JAN 2013 | DOI: 10.1002/jcc.23199

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      Ligand parameterization for molecular mechanics simulations is computationally intensive, requiring long multistep optimization procedures. Recently there has been an influx of automated parameterization tools for the CHARMM force field. These tools radically speed up the process, but it remains unclear whether accuracy is sacri- ficed to a significant extent. The research presented in this article uses a set of 457 small molecules to quantify the accuracy of four automated parameterization tools by computing absolute hydration free energies.

    2. Advanced techniques for constrained internal coordinate molecular dynamics (pages 904–914)

      Jeffrey R. Wagner, Gouthaman S. Balaraman, Michiel J. M. Niesen, Adrien B. Larsen, Abhinandan Jain and Nagarajan Vaidehi

      Version of Record online: 23 JAN 2013 | DOI: 10.1002/jcc.23200

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      Unlike the widely used all-atom unconstrained Cartesian molecular dynamics, internal coordinate molecular dynamics (ICMD) methods use bond, angle, and torsional coordinates for a more natural description of the protein. Solutions to several theoretical problems are implemented to make the constrained ICMD method robust and widely usable. These methods are further validated using simulations of proteins, and constrained ICMD is applied to ab initio protein folding.

    3. Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines (pages 915–927)

      Xiaohua Zhang, Sergio E. Wong and Felice C. Lightstone

      Version of Record online: 23 JAN 2013 | DOI: 10.1002/jcc.23214

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      A popular PC-based molecular docking program, AutoDock Vina, is modified and parallelized using an MPI and multithreading hybrid scheme, and potentially can be used on exascale machines without sacri- ficing accuracy. The resulting program scales up to more than 15K CPUs with a very low overhead cost.

    4. Adjustment of Born-Oppenheimer electronic wave functions to simplify close coupling calculations (pages 928–937)

      Robert J. Buenker, Heinz-Peter Liebermann, Yu Zhang, Yong Wu, Lingling Yan, Chunhua Liu, Yizhi Qu and Jianguo Wang

      Version of Record online: 23 JAN 2013 | DOI: 10.1002/jcc.23215

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      The Born-Oppenheimer clamped nuclei approximation generates electronic wave functions at each internuclear geometry, regard less of results obtained at neighboring points (single-point method). This procedure generally leads to discontinuous behavior of both the wave functions and associated properties such as off-diagonal nonadiabatic couplings and transition moments. For the first time an algorithm is presented for guaranteeing continuity of all these quantities over the entire range of nuclear geometries considered.

    5. Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond (pages 938–951)

      Anthony Scemama, Michel Caffarel, Emmanuel Oseret and William Jalby

      Version of Record online: 3 JAN 2013 | DOI: 10.1002/jcc.23216

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      Various optimizations and strategies are implemented in the QMC=Chem code for simulating large systems. These are illustrated with numerical applications on small peptides of increasing sizes (158–1731 electrons). Using 10–80 k computing cores of the Curie machine (GENCI-TGCCCEA, France), QMC=Chem is shown to be capable of running at the petascale level, thus demonstrating that, for this machine, a large part of the peak performance can be achieved.

    6. After the electronic field: Structure, bonding, and the first hyperpolarizability of HArF (pages 952–957)

      Heng-Qing Wu, Rong-Lin Zhong, Yu-He Kan, Shi-Ling Sun, Min Zhang, Hong-Liang Xu and Zhong-Min Su

      Version of Record online: 3 JAN 2013 | DOI: 10.1002/jcc.23220

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      A physical method of external electric field (Eext) is put forward to investigate the HArF structure. The NBO analyses show that the charges of the F atom range from –0.961 to –0.771, and the charges of H atoms range from 0.402 to 0.246. Due to the weakened charge transfer, the first hyperpolarizabilities range from 4078 to 1087 au, which indicates that first hyperpolarizability can be modulated by controlling the HArF structure.

    7. Long-range corrected functionals satisfy Koopmans' theorem: Calculation of correlation and relaxation energies (pages 958–964)

      Rahul Kar, Jong-Won Song and Kimihiko Hirao

      Version of Record online: 8 JAN 2013 | DOI: 10.1002/jcc.23222

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      Long-range corrected density functionals are shown to satisfy Koopmans' theorem by reproducing frontier orbital energies. Relaxation and correlation energy for 113 molecules are calculated and compared with other density functionals and the Hartree-Fock method.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. FEW: A workflow tool for free energy calculations of ligand binding (pages 965–973)

      Nadine Homeyer and Holger Gohlke

      Version of Record online: 3 JAN 2013 | DOI: 10.1002/jcc.23218

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      Given a set of ligand structures and a receptor structure the “free energy Work- flow” (FEW) tool prepares and analyzses binding free energy calculations for the AMBER suite of programs. The automated process greatly reduces the complexity and the time needed for setup, execution, and analysis of calculations according to the MM-PB(GB)SA, the linear interaction energy, and the thermodynamic integration approach.

    2. TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble (pages 974–985)

      Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhen-Min Tang and Jing-Yu Yang

      Version of Record online: 3 JAN 2013 | DOI: 10.1002/jcc.23219

      Thumbnail image of graphical abstract

      Accurately localizing the protein-ATP binding sites is important for protein function analysis and drug design. A template-free machine learning-based software named TargetATPsite is developed to predict protein- ATP binding residues and pockets from amino acid sequences. The binding residues are predicted by an ensemble classifier formed by support vector machines, and the input features are sparse representations of residue evolution images. Binding pockets are identified through spatially clustering predicted binding residues.

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