Wiley Interdisciplinary Reviews: Computational Molecular Science

Cover image for Vol. 7 Issue 4

Early View (Online Version of Record published before inclusion in an issue)

Editor-in-Chief: Peter R. Schreiner

Impact Factor: 14.016

ISI Journal Citation Reports © Ranking: 2016: 1/57 (Mathematical & Computational Biology); 8/166 (Chemistry Multidisciplinary)

Online ISSN: 1759-0884

Associated Title(s): Journal of Computational Chemistry, Molecular Informatics

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  1. Overviews

    1. Molecular electrostatic potentials and noncovalent interactions

      Jane S. Murray and Peter Politzer

      Version of Record online: 18 JUL 2017 | DOI: 10.1002/wcms.1326

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      The most positive regions of electrostatic potential on molecular surfaces (shown in red) are often associated with regions of lower electronic density that are approximately along the extensions of bonds (σ-holes) or perpendicular to planar portions of the molecular framework (π-holes).

  2. Software Focus

    1. Software update: the ORCA program system, version 4.0

      Frank Neese

      Version of Record online: 17 JUL 2017 | DOI: 10.1002/wcms.1327

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      The quantum chemistry program suite ORCA, version 4.0 is described in this article.

  3. Advanced Reviews

    1. The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

      Dmitri G. Fedorov

      Version of Record online: 20 JUN 2017 | DOI: 10.1002/wcms.1322

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      The properties (here, energy E and electron density ρ ) are expanded in fragment molecular orbital (FMO) into a series with the contributions from isolated fragments, polarization, two- and three-body charge transfer and exchange-repulsion, drawn in scale (50×, etc.).

  4. Opinion

    1. Recent advances in dynamic docking for drug discovery

      Marco De Vivo and Andrea Cavalli

      Version of Record online: 13 JUN 2017 | DOI: 10.1002/wcms.1320

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      Dynamic docking for drug discovery.

  5. Advanced Reviews

    1. Theory and applications of surface micro-kinetics in the rational design of catalysts using density functional theory calculations

      Yu Mao, Hai-Feng Wang and P. Hu

      Version of Record online: 5 JUN 2017 | DOI: 10.1002/wcms.1321

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      Schematic representation of the Sabatier's principle and the volcano curve.

    2. The divide–expand–consolidate coupled cluster scheme

      Thomas Kjærgaard, Pablo Baudin, Dmytro Bykov, Kasper Kristensen and Poul Jørgensen

      Version of Record online: 5 JUN 2017 | DOI: 10.1002/wcms.1319

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      The divide–expand–consolidate (DEC) scheme is a linear-scaling and massively parallel framework for high accuracy coupled cluster (CC) calculations on large molecular systems.

    3. Recent advances in the prediction of non-CYP450-mediated drug metabolism

      Vaibhav A. Dixit, L. Arun Lal and Simran R. Agrawal

      Version of Record online: 2 JUN 2017 | DOI: 10.1002/wcms.1323

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      Developments in the computational prediction of drug metabolism by non-CYP450 enzymes have been slow, but recent recognition of toxicity has given impetus. Recent developments in this area are discussed and urgent need for the development of sequential and comprehensive models for Phase I and Phase II metabolic processes is highlighted.

    4. Protein design: from computer models to artificial intelligence

      Antonella Paladino, Filippo Marchetti, Silvia Rinaldi and Giorgio Colombo

      Version of Record online: 24 MAY 2017 | DOI: 10.1002/wcms.1318

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      Design of proteins with desired functions is within reach thanks to the combination of computational biology and computer learning.

  6. Focus Articles

    1. About P-glycoprotein: a new drugable domain is emerging from structural data

      Ricardo J. Ferreira, Cátia A. Bonito, Maria José U. Ferreira and Daniel J.V.A. dos Santos

      Version of Record online: 4 MAY 2017 | DOI: 10.1002/wcms.1316

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      New studies identified a specific domain within the P-glycoprotein structure that can block conformational changes leading to efflux.

  7. Overviews

    1. Polarizable force field development for lipids and their efficient applications in membrane proteins

      Huiying Chu, Liaoran Cao, Xiangda Peng and Guohui Li

      Version of Record online: 26 APR 2017 | DOI: 10.1002/wcms.1312

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      The ball-and-stick scheme of a lipid bilayer molecule and its corresponding electrostatic potential surface under polarizable force field.

  8. Advanced Reviews

    1. Prospects of spintronics based on 2D materials

      Yuan Ping Feng, Lei Shen, Ming Yang, Aizhu Wang, Minggang Zeng, Qingyun Wu, Sandhya Chintalapati and Ching-Ray Chang

      Version of Record online: 21 APR 2017 | DOI: 10.1002/wcms.1313

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      Spin-dependent transport property of zigzag graphene nanoribbon and schematics of theoretical design of spintronic device element (insets). The spin-polarization and flow direction of electric current in the graphene nanoribbon can be controlled by magnetization of the electrodes and the bias voltage, allowing implementation of spin logic gates. image, spin up, antiparallel magnetization; image, spin down, antiparallel magnetization; image, spin up, parallel magnetization; image, spin down, parallel magnetization.

    2. Accelerating physical simulations of proteins by leveraging external knowledge

      Alberto Perez, Joseph A. Morrone and Ken A. Dill

      Version of Record online: 19 APR 2017 | DOI: 10.1002/wcms.1309

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      Board games such as chess and Go have been computational grand challenges because of the large number of options to explore. Computer successes in defeating human grand masters were not just because of raw hardware power, but also due to clever heuristics. Folding proteins requires surmounting even bigger computational search problems, even though nature finds those states through physics rapidly, usually within seconds. A broad range of STEM problems could benefit from combining physics with new heuristics approaches.

    3. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here?

      Adam W. Duster, Chun-Hung Wang, Christina M. Garza, Danielle E. Miller and Hai Lin

      Version of Record online: 17 APR 2017 | DOI: 10.1002/wcms.1310

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      Adaptive QM/MM reclassifies atoms as QM or MM on the fly in a smooth manner during dynamics simulations, allowing the location and contents of the QM subsystem to be updated as needed.

    4. 3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

      François Le Dily, François Serra and Marc A. Marti-Renom

      Version of Record online: 10 APR 2017 | DOI: 10.1002/wcms.1308

      Thumbnail image of graphical abstract

      Graphical comparison of the two orthogonal ways of interrogating the genome three-dimensional structure. Left panel depicts frequency of cross-linking with respect the genomic distance of the interacting loci in a typical 3C-based experiment. Right panel represents a typical image from light microscopy depicting distance of loci in a chromosome.

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