Journal of Computational Chemistry

Cover image for Vol. 37 Issue 28

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

Impact Factor: 3.648

ISI Journal Citation Reports © Ranking: 2015: 40/163 (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. A pH-dependent computational approach to the effect of mutations on protein stability

    Velin Z. Spassov and Lisa Yan

    Version of Record online: 16 SEP 2016 | DOI: 10.1002/jcc.24482

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    The search for protein variants with improved stability is a particularly challenging task in rational protein design. Here, we report a novel computational approach that addresses this task via high-throughput combinatorial scanning mutagenesis. In addition to predicting the free energy differences on mutations, the pH-dependent model makes it possible to evaluate a number of other protein properties such as the pK's of the acidic and basic residues and corresponding titration curves without additional calculations.

  2. Massively parallel algorithm and implementation of RI-MP2 energy calculation for peta-scale many-core supercomputers

    Michio Katouda, Akira Naruse, Yukihiko Hirano and Takahito Nakajima

    Version of Record online: 16 SEP 2016 | DOI: 10.1002/jcc.24491

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    A new parallel algorithm and its implementation for the RI-MP2 energy calculation utilizing peta-flop-class many-core supercomputers are presented. In this algorithm, (1) a dual-level hierarchical parallelization scheme that enables the use of more than 10,000 MPI processes and (2) a new data communication scheme that reduces network communication overhead are applied. Benchmark calculations using the new implementation on the K computer (CPU clustering system) and TSUBAME 2.5 (CPU/GPU hybrid system) demonstrate high parallel efficiency.

  3. You have full text access to this OnlineOpen article
    Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

    Michael M. H. Graf, Manuela Maurer and Chris Oostenbrink

    Version of Record online: 16 SEP 2016 | DOI: 10.1002/jcc.24488

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    Sampling problems hamper accurate calculation of free energy differences in many systems. Here, a residue transformation of a simple tripeptide system is presented, for which free energy differences are surprisingly difficult to compute. The reasons for these difficulties are elucidated and possible approaches to circumvent them are introduced.

  4. Horizontal vectorization of electron repulsion integrals (pages 2537–2546)

    Benjamin P. Pritchard and Edmond Chow

    Version of Record online: 13 SEP 2016 | DOI: 10.1002/jcc.24483

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    Speedup of the computation of electron repulsion integrals can be obtained by utilizing horizontal vectorization of the primitive loop in the Obara–Saika algorithm. In this scheme, multiple primitive integrals are calculated concurrently within a SIMD word. The algorithm has been implemented in a new library called Simint. Comparisons against scalar code display favorable results.

  5. Exponential repulsion improves structural predictability of molecular docking (pages 2485–2494)

    Václav Bazgier, Karel Berka, Michal Otyepka and Pavel Banáš

    Version of Record online: 13 SEP 2016 | DOI: 10.1002/jcc.24473

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    This study presents implementation and testing of scoring function based on AMBER force field with AMBER-like arithmetic mixing rules and more physically justified exponential repulsion instead of standard 6–12 Lennard–Jones potential. Several robust tests showed that the scoring function with exponential repulsion improves prediction of native binding poses in proteins bearing narrow and polar active sites such as serine proteases and kinases.

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