Israel Journal of Chemistry

Cover image for Vol. 54 Issue 8‐9

Special Issue: Computational Molecular Biophysics

August 2014

Volume 54, Issue 8-9

Pages 1027–1403

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Contents
    4. Masthead
    5. Guest Editorial
    6. Reviews
    7. Full Papers
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      Cover Picture: Computational Molecular Biophysics: 40 Years of Achievements (Isr. J. Chem. 8-9/2014) (page 1027)

      Yaakov Levy and Jeffrey Skolnick

      Version of Record online: 15 SEP 2014 | DOI: 10.1002/ijch.201490015

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      This special volume focuses on Computational molecular biophysics in honor of the 2013 Nobel Prize in Chemistry awarded to Karplus (right), Levitt (middle), and Warshel (left). In a series of seminal contributions, the three laureates provided novel approaches to study complex chemical systems. The cover shows the fundamental energy terms used in many transferrable force-fields to calculate the structure of a variety of biomolecules. Force-fields are still widely used, both in atomistic or coarse-grained forms, to decipher the conformational landscape (represented by the white curve) of proteins and their folding mechanism. The cover also illustrates the achievement of the Nobel laureates to study the action of an enzyme (the cover highlights Lysozyme that breaks polysaccharides into smaller fragments) by carefully integrating quantum and classical calculations. See the Guest Editorial on page 1039.

  2. Contents

    1. Top of page
    2. Cover Picture
    3. Contents
    4. Masthead
    5. Guest Editorial
    6. Reviews
    7. Full Papers
    1. You have free access to this content
  3. Masthead

    1. Top of page
    2. Cover Picture
    3. Contents
    4. Masthead
    5. Guest Editorial
    6. Reviews
    7. Full Papers
  4. Guest Editorial

    1. Top of page
    2. Cover Picture
    3. Contents
    4. Masthead
    5. Guest Editorial
    6. Reviews
    7. Full Papers
    1. You have free access to this content
  5. Reviews

    1. Top of page
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    3. Contents
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    5. Guest Editorial
    6. Reviews
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    1. Significance of Molecular Dynamics Simulations for Life Sciences (pages 1042–1051)

      Martin Karplus and Richard Lavery

      Version of Record online: 8 AUG 2014 | DOI: 10.1002/ijch.201400074

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    2. Communication Maps: Exploring Energy Transport through Proteins and Water (pages 1065–1073)

      Johnson K. Agbo, Ramachandran Gnanasekaran and David M. Leitner

      Version of Record online: 1 APR 2014 | DOI: 10.1002/ijch.201300139

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    3. The Treatment of Solvent in Multiscale Biophysical Modeling (pages 1074–1083)

      Themis Lazaridis and Rodney Versace

      Version of Record online: 6 APR 2014 | DOI: 10.1002/ijch.201400006

    4. Multiscale Quantum-Classical Simulations of Enzymes (pages 1108–1117)

      Dvir Doron, Michal Weitman, Alexandra Vardi-Kilshtain, Asaf Azuri, Hamutal Engel and Dan T. Major

      Version of Record online: 11 APR 2014 | DOI: 10.1002/ijch.201400026

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    5. Folding of Right- and Left-Handed Three-Helix Proteins (pages 1126–1136)

      Oxana V. Galzitskaya, Leonid B. Pereyaslavets and Anna V. Glyakina

      Version of Record online: 2 MAY 2014 | DOI: 10.1002/ijch.201300146

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    6. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases (pages 1137–1151)

      Michael Shokhen, Michal Hirsch, Netaly Khazanov, Rachel Ozeri, Nurit Perlman, Tamar Traube, Subramaniam Vijayakumar and Amnon Albeck

      Version of Record online: 12 MAY 2014 | DOI: 10.1002/ijch.201300144

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    7. Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding (pages 1152–1164)

      Jessica D. Leuchter, Adam T. Green, Julian Gilyard, Cecilia G. Rambarat and Samuel S. Cho

      Version of Record online: 13 MAY 2014 | DOI: 10.1002/ijch.201400022

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    8. Simulating Biomolecular Folding and Function by Native-Structure-Based/Go-Type Models (pages 1165–1175)

      Claude Sinner, Benjamin Lutz, Shalini John, Ines Reinartz, Abhinav Verma and Alexander Schug

      Version of Record online: 26 JUN 2014 | DOI: 10.1002/ijch.201400012

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    9. Computational Studies of Smell and Taste Receptors (pages 1205–1218)

      Antonella Di Pizio and Masha Y. Niv

      Version of Record online: 28 JUL 2014 | DOI: 10.1002/ijch.201400027

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    10. Whole Cell Modeling: From Single Cells to Colonies (pages 1219–1229)

      John A. Cole and Zaida Luthey-Schulten

      Version of Record online: 31 JUL 2014 | DOI: 10.1002/ijch.201300147

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    11. Modeling Non-Native Interactions in Designed Proteins (pages 1230–1240)

      Shilpa Yadahalli, V. V. Hemanth Giri Rao and Shachi Gosavi

      Version of Record online: 31 JUL 2014 | DOI: 10.1002/ijch.201400035

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    12. Knotted Proteins under Tension (pages 1241–1249)

      Mateusz Chwastyk and Marek Cieplak

      Version of Record online: 31 JUL 2014 | DOI: 10.1002/ijch.201400004

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    13. QM/MM through the 1990s: The First Twenty Years of Method Development and Applications (pages 1250–1263)

      Meiyi Liu, Yingjie Wang, Yakun Chen, Martin J. Field and Jiali Gao

      Version of Record online: 31 JUL 2014 | DOI: 10.1002/ijch.201400036

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    14. Biomolecular Structure and Dynamics with Neutrons: The View from Simulation (pages 1264–1273)

      Liang Hong, Loukas Petridis and Jeremy C. Smith

      Version of Record online: 31 JUL 2014 | DOI: 10.1002/ijch.201300137

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    15. Structural Heterogeneity and Dynamics of the Unfolded Ensemble (pages 1293–1301)

      Ignacia Echeverria and Garegin A. Papoian

      Version of Record online: 18 AUG 2014 | DOI: 10.1002/ijch.201400030

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    16. Molecular Dynamics at Extended Timescales (pages 1302–1310)

      Ron Elber and Alfredo E. Cardenas

      Version of Record online: 20 AUG 2014 | DOI: 10.1002/ijch.201400015

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    17. Learning To Fold Proteins Using Energy Landscape Theory (pages 1311–1337)

      Nicholas P. Schafer, Bobby L. Kim, Weihua Zheng and Peter G. Wolynes

      Version of Record online: 20 AUG 2014 | DOI: 10.1002/ijch.201300145

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    18. Development and Applications of Coarse-Grained Models for RNA (pages 1358–1373)

      Changbong Hyeon, Natalia A. Denesyuk and D. Thirumalai

      Version of Record online: 21 AUG 2014 | DOI: 10.1002/ijch.201400029

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  6. Full Papers

    1. Top of page
    2. Cover Picture
    3. Contents
    4. Masthead
    5. Guest Editorial
    6. Reviews
    7. Full Papers
    1. Structural Characterization of the Drug Translocation Path of MRP1/ABCC1 (pages 1382–1393)

      Shay Amram, Assaf Ganoth, Or Tichon, Dan Peer, Esther Nachliel, Menachem Gutman and Yossi Tsfadia

      Version of Record online: 12 MAY 2014 | DOI: 10.1002/ijch.201300132

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