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There are 6779 results for: content related to: Quaternion-based definition of protein secondary structure straightness and its relationship to Ramachandran angles

  1. Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity

    Proteins: Structure, Function, and Bioinformatics

    Volume 40, Issue 4, 1 September 2000, Pages: 543–571, Hue Sun Chan

    Article first published online : 28 JUN 2000, DOI: 10.1002/1097-0134(20000901)40:4<543::AID-PROT20>3.0.CO;2-O

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    Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 5, April 2010, Pages: 1212–1227, Benjamin M. Messer, Maite Roca, Zhen T. Chu, Spyridon Vicatos, Alexandra Vardi Kilshtain and Arieh Warshel

    Article first published online : 16 OCT 2009, DOI: 10.1002/prot.22640

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    Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins

    Proteins: Structure, Function, and Bioinformatics

    Volume 66, Issue 1, January 2007, Pages: 29–40, Lerzan Ormeci, Attila Gursoy, Guzin Tunca and Burak Erman

    Article first published online : 12 OCT 2006, DOI: 10.1002/prot.21206

  4. Protein conformational transitions explored by mixed elastic network models

    Proteins: Structure, Function, and Bioinformatics

    Volume 69, Issue 1, October 2007, Pages: 43–57, Wenjun Zheng, Bernard R. Brooks and Gerhard Hummer

    Article first published online : 27 JUN 2007, DOI: 10.1002/prot.21465

  5. Iterative cluster-NMA: A tool for generating conformational transitions in proteins

    Proteins: Structure, Function, and Bioinformatics

    Volume 74, Issue 3, 15 February 2009, Pages: 760–776, Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan and Gregory S. Chirikjian

    Article first published online : 19 AUG 2008, DOI: 10.1002/prot.22200

  6. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein–protein association using MM-GBSA: Application to the TCR-p-MHC complex

    Proteins: Structure, Function, and Bioinformatics

    Volume 67, Issue 4, June 2007, Pages: 1026–1047, Vincent Zoete and Olivier Michielin

    Article first published online : 21 MAR 2007, DOI: 10.1002/prot.21395

  7. Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space

    Proteins: Structure, Function, and Bioinformatics

    Volume 75, Issue 3, 15 May 2009, Pages: 682–705, Menachem Fromer and Chen Yanover

    Article first published online : 25 SEP 2008, DOI: 10.1002/prot.22280

  8. Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

    Proteins: Structure, Function, and Bioinformatics

    Volume 79, Issue 9, September 2011, Pages: 2648–2661, Sheng-You Huang and Xiaoqin Zou

    Article first published online : 5 JUL 2011, DOI: 10.1002/prot.23086

  9. Structural thermodynamics of protein preferential solvation: Osmolyte solvation of proteins, aminoacids, and peptides

    Proteins: Structure, Function, and Bioinformatics

    Volume 73, Issue 4, December 2008, Pages: 802–813, Matthew Auton, D. Wayne Bolen and Jörg Rösgen

    Article first published online : 22 MAY 2008, DOI: 10.1002/prot.22103

  10. Effective approach for calculations of absolute stability of proteins using focused dielectric constants

    Proteins: Structure, Function, and Bioinformatics

    Volume 77, Issue 3, 15 November 2009, Pages: 670–684, Spyridon Vicatos, Maite Roca and Arieh Warshel

    Article first published online : 18 MAY 2009, DOI: 10.1002/prot.22481

  11. Robustness and generalization of structure-based models for protein folding and function

    Proteins: Structure, Function, and Bioinformatics

    Volume 77, Issue 4, December 2009, Pages: 881–891, Heiko Lammert, Alexander Schug and José N. Onuchic

    Article first published online : 19 JUN 2009, DOI: 10.1002/prot.22511

  12. Folding and dimerization of the ionic peptide EAK 16-IV

    Proteins: Structure, Function, and Bioinformatics

    Volume 72, Issue 1, July 2008, Pages: 150–162, Zhiqiang Yan, Jun Wang and Wei Wang

    Article first published online : 23 JAN 2008, DOI: 10.1002/prot.21903

  13. Backbone dynamics of TFE-induced native-like fold of region 4 of Escherichia coli RNA polymerase σ70 subunit

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 3, 15 February 2010, Pages: 754–768, Piotr Kaczka, Agnieszka Polkowska-Nowakowska, Krystyna Bolewska, Igor Zhukov, Jarosław Poznański and Kazimierz L. Wierzchowski

    Article first published online : 11 SEP 2009, DOI: 10.1002/prot.22607

  14. Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F1 ATPase

    Proteins: Structure, Function, and Bioinformatics

    Volume 76, Issue 3, 15 August 2009, Pages: 747–762, Wenjun Zheng

    Article first published online : 2 FEB 2009, DOI: 10.1002/prot.22386

  15. Unstructured intermediate states in single protein force experiments

    Proteins: Structure, Function, and Bioinformatics

    Volume 71, Issue 3, 15 May 2008, Pages: 1145–1155, Ivan Junier and Felix Ritort

    Article first published online : 14 NOV 2007, DOI: 10.1002/prot.21802

  16. Optimizing pKA computation in proteins with pH adapted conformations

    Proteins: Structure, Function, and Bioinformatics

    Volume 71, Issue 3, 15 May 2008, Pages: 1335–1348, Gernot Kieseritzky and Ernst-Walter Knapp

    Article first published online : 3 DEC 2007, DOI: 10.1002/prot.21820

  17. Do collagenases unwind triple-helical collagen before peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models

    Proteins: Structure, Function, and Bioinformatics

    Volume 70, Issue 4, March 2008, Pages: 1154–1161, Paul S. Nerenberg, Ramon Salsas-Escat and Collin M. Stultz

    Article first published online : 11 OCT 2007, DOI: 10.1002/prot.21687

  18. Self-guided Langevin dynamics study of regulatory interactions in NtrC

    Proteins: Structure, Function, and Bioinformatics

    Volume 76, Issue 4, September 2009, Pages: 1007–1019, Ana Damjanović, Bertrand García-Moreno E. and Bernard R. Brooks

    Article first published online : 26 MAR 2009, DOI: 10.1002/prot.22439

  19. Lipid a from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulations

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 4, April 2013, Pages: 658–674, Jose Antonio Garate and Chris Oostenbrink

    Article first published online : 15 JAN 2013, DOI: 10.1002/prot.24223

  20. Graphical models of protein–protein interaction specificity from correlated mutations and interaction data

    Proteins: Structure, Function, and Bioinformatics

    Volume 76, Issue 4, September 2009, Pages: 911–929, John Thomas, Naren Ramakrishnan and Chris Bailey-Kellogg

    Article first published online : 2 FEB 2009, DOI: 10.1002/prot.22398