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S. Banu Ozkan, G. Albert Wu, John D. Chodera and Ken A. Dill Proceedings of the National Academy of Sciences 104(29) 11987 (2007) https://doi.org/10.1073/pnas.0703700104
A unified mechanism for protein folding: Predetermined pathways with optional errors
Use of the Novel Fluorescent Amino Acid p-Cyanophenylalanine Offers a Direct Probe of Hydrophobic Core Formation during the Folding of the N-Terminal Domain of the Ribosomal Protein L9 and Provides Evidence for Two-State Folding
Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach
Elad Segev, Mikael Grumbach and Robert Benny Gerber Physical Chemistry Chemical Physics 8(42) 4915 (2006) https://doi.org/10.1039/b610872e
Fundamental processes of protein folding: Measuring the energetic balance between helix formation and hydrophobic interactions
Wujing Xian, Peter J. Connolly, Marcela Oslin, Andrew C. Hausrath and John J. Osterhout Protein Science 15(9) 2062 (2006) https://doi.org/10.1110/ps.062297006
Protein Folding Pathways Studied by Pulsed- and Native-State Hydrogen Exchange
Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1
J.B. Abrams, M.E. Tuckerman and G.J. Martyna Lecture Notes in Physics, Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1 703 139 (2006) https://doi.org/10.1007/3-540-35273-2_5
Substructural cooperativity and parallel versus sequential events during protein unfolding
Order of Steps in the Cytochrome c Folding Pathway: Evidence for a Sequential Stabilization Mechanism
Mallela M.G. Krishna, Haripada Maity, Jon N. Rumbley, Yan Lin and S. Walter Englander Journal of Molecular Biology 359(5) 1410 (2006) https://doi.org/10.1016/j.jmb.2006.04.035
Relationships between the folding rate constant and the topological parameters of small two-state proteins based on general random walk model
Maxim S. Pometun, Ronald W. Peterson, Charles R. Babu and A. Joshua Wand Journal of the American Chemical Society 128(33) 10652 (2006) https://doi.org/10.1021/ja0628654
Encyclopedia of Molecular Cell Biology and Molecular Medicine
Criteria for downhill protein folding: Calorimetry, chevron plot, kinetic relaxation, and single‐molecule radius of gyration in chain models with subdued degrees of cooperativity
2,2,2-Trifluoroethanol-Induced Molten Globule State of Concanavalin A and Energetics of 8-Anilinonaphthalene Sulfonate Binding: Calorimetric and Spectroscopic Investigation
Identification of residual structure within denatured antichymotrypsin: implications for serpin folding and misfolding
Mary C. Pearce, Lisa D. Cabrita, Harvey Rubin, Michael G. Gore and Stephen P. Bottomley Biochemical and Biophysical Research Communications 324(2) 729 (2004) https://doi.org/10.1016/j.bbrc.2004.09.105
Experimental and Theoretical Studies of Protein Folding‐Unfolding
Y. J. Shiu, Catherlene Su, Y. L. Yeh, K. K. Liang, M. Hayashi, Yan Mo, Yijing Yan and S. H. Lin Journal of the Chinese Chemical Society 51(5B) 1161 (2004) https://doi.org/10.1002/jccs.200400172
The World of β‐ and γ‐Peptides Comprised of Homologated Proteinogenic Amino Acids and Other Components
Protein–Protein Recognition: Juxtaposition of Domain and Interface Cores in Immunoglobulins and Other Sandwich-like Proteins
Vladimir Potapov, Vladimir Sobolev, Marvin Edelman, Alexander Kister and Israel Gelfand Journal of Molecular Biology 342(2) 665 (2004) https://doi.org/10.1016/j.jmb.2004.06.072
Funnel‐like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution
Water–protein interactions from high–resolution protein crystallography
Masayoshi Nakasako, R. M. Daniel, J. L. Finney and M. Stoneham Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359(1448) 1191 (2004) https://doi.org/10.1098/rstb.2004.1498
Fast folding dynamics of an α-helical peptide with bulky side chains
Phylogeny of protein-folding trajectories reveals a unique pathway to native structure
Motonori Ota, Mitsunori Ikeguchi and Akinori Kidera Proceedings of the National Academy of Sciences 101(51) 17658 (2004) https://doi.org/10.1073/pnas.0407015102
Mesoscopic analysis of conformational and entropic contributions to nonspecific adsorption of HP copolymer chains using dynamic Monte Carlo simulations
Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
Adam Liwo, Piotr Arłukowicz, Stanisław Ołdziej, et al. The Journal of Physical Chemistry B 108(43) 16918 (2004) https://doi.org/10.1021/jp040327c
Apo‐azurin folds via an intermediate that resembles the molten‐globule
Unfolded state of polyalanine is a segmented polyproline II helix
Alex Kentsis, Mihaly Mezei, Tatyana Gindin and Roman Osman Proteins: Structure, Function, and Bioinformatics 55(3) 493 (2004) https://doi.org/10.1002/prot.20051
Brute-Force Molecular Dynamics Simulations of Villin Headpiece: Comparison with NMR Parameters
The SAAP force field. A simple approach to a new all‐atom protein force field by using single amino acid potential (SAAP) functions in various solvents*