JOURNAL ARTICLES BOOK CHAPTERS CONFERENCE PROCEEDINGS ARTICLES

    P. Kota, D. Summers, H.-Y. Ren, D. M. Cyr, and N. V. Dokholyan, "Identification of a consensus motif in substrates bound by a Type I Hsp40" Proceedings of the National Academy of Sciences USA, in press (2009)

    B. A. Kesner, F. Ding, B. S. Temple, and N. V. Dokholyan, "N-terminal strands of filamin Ig domains act as a conformational switch under biological forces" Proteins: Structure, Function, and Bioinformatics, in press (2009)
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    A. W. R. Serohijos, D. Tsygankov, S. Liu, T. C. Elston, and N. V. Dokholyan, "Multiscale approaches for studying energy transduction in dynein" Physical Chemistry Chemical Physics, in press (2009)
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    K. Wilcox, L. Zhou, J. Jordon, Y. Huang, Y. Yu, R. L. Redler, X. Chen, M. Caplow, and N. V. Dokholyan, "Modifications of SOD1 in human erythrocytes: A possible role in ALS" Journal of Biological Chemistry, 284: 13940-13947 (2009)
    [Adobe PDF][Supporting Information, Adobe PDF]

    S. Ramachandran, A. W. R. Serohijos, L. Xu, G. Meissner, and N. V. Dokholyan, "Ryanodine receptor pore structure and function" Public Library of Science Computational Biology, 5: e1000367 (2009)
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    M. P. Torres, M. J. Lee, F. Ding, C. Purbeck, B. Kuhlman, N. V. Dokholyan, and H. G. Dohlman, "G protein mono-ubiquitination by the Rsp5 ubiquitin ligase" Journal of Biological Chemistry, 284: 8940-8950 (2009)
    [Adobe PDF][Supporting Information, Adobe PDF]

    S. Ramachandran, B. Temple, S. G. Chaney, and N. V. Dokholyan, "Structural basis for the sequence dependent effects of platinum-DNA adducts" Nucleic Acids Research, 37: 2434-2448 (2009)
    [Adobe PDF][Supporting Information, Adobe PDF]

    C. M. Gherghe, C. W. Leonard, F. Ding, N. V. Dokholyan, and K. M. Weeks, "Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics" Journal of the American Chemical Society, 131: 25412546 (2009)
    [Adobe PDF][Supporting Information, Adobe PDF]

    T. Schwede, A. Sali, B. Honig, M. Levitt, H. M. Berman, B. Jones, S. Brenner, S. K. Burley, R. Das, N. V. Dokholyan, R. L. Dunbrack Jr., K. Fidelis, A. Fiser, A. Godzik, C. Humblet, M. P. Jacobson, A. Joachimiak, S. Krystek, T. Kortemme, A. Kryshtafovych, G. Montelione, J. Moult, D. Murray, R. Sanchez, T. R. Sosnick, D. M. Standley, T. Stouch, S. Vajda, J. D. Westbrook, and I. A. Wilson, "Outcome of a workshop on applications of protein models in biomedical research" Structure, 17: 151-159 (2009)
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    D. Tsygankov, A. W. R. Serohijos, N. V. Dokholyan, and T. C. Elston, "Kinetic models for the coordinated stepping of cytoplasmic dynein" Journal of Chemical Physics, 130: 25101 (2009)
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    G. Meissner, D. A. Pasek, N. Yamaguchi, S. Ramachandran, N. V. Dokholyan, and A. Tripathy, "Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels" Proteins: Structure, Function, and Bioinformatics, 74: 207-211 (2009)
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    E. V. Petrotchenko, K. Xiao, J. Cable, Y. Chen, N. V. Dokholyan, and C. H. Borchers, "Bimane Bisthiopropionic Acid N-Succinimidyl Ester (BiPS), a photo-cleavable, isotopically-coded, fluorescent crosslinker for structural proteomics" Molecular & Cellular Proteomics, 8: 273-286 (2009) [Cover article]
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    F. Ding and N. V. Dokholyan, "Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation" Proceedings of the National Academy of Sciences USA, 105: 19696-19701 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF]

    L. He, A. W. R. Serohijos, T. Hegedus, L. A. Aleksandrov, L. Cui, A. A. Aleksandrov, N. V. Dokholyan, and J. R. Riordan, "Multiple membrane-cytoplasmic domain contacts in CFTR" Journal of Biological Chemistry, 283: 26383-26390 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF]

    C. Ozvegy-Laczka, R. Laczko, C. Hegedus, T. Litman, G. Varady, K. Goda, T. Hegedus, N. V. Dokholyan, B. P. Sorrentino, A. Varadi, and B. Sarkadi, "Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter" Journal of Biological Chemistry, 283: 26059-26070 (2008)
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    S. Yin, L. Biedermannova, J. Vondrasek, and N. V. Dokholyan, "MedusaScore: An accurate force-field based scoring function for virtual drug screening" Journal of Chemical Information and Modeling, 48: 1656-1662 (2008)
    [Adobe PDF] [Supporting Information, Adobe PDF]

    S. Sharma, F. Ding, and N. V. Dokholyan, "iFoldRNA: Three-dimensional RNA structure prediction and folding" Bioinformatics, 24: 1951-1952 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF][Portal: iFoldRNA]

    J. Hao, A. W. R. Serohijos, G. Newton, G. Tassone, Z. Wang, D. C. Sgroi, N. V. Dokholyan, and J. P. Basilion, "Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers" Public Library of Science Computational Biology, 4: e1000138 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF]

    Y. Chen and N. V. Dokholyan, "Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly and worm" Molecular Biology and Evolution, 25: 1530-1533 (2008)
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    D. G. Teotico, M. Frazier, F. Ding, N. V. Dokholyan, B. Temple, and M. R. Redinbo, "Active nuclear receptors exhibit highly correlated AF-2 domain motions" Public Library of Science Computational Biology, 4: e1000111 (2008) [Cover article]
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    F. Ding, D. Tsao, H. Nie, and N. V. Dokholyan, "Ab initio folding of proteins with all-atom discrete molecular dynamics" Structure, 16: 1010-1018 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF]

    T. Hegedus, A. W. R. Serohijos, N. V. Dokholyan, L. He, and J. R. Riordan, "Computational studies reveal phosphorylation dependent changes in the unstructured R domain of CFTR" Journal of Molecular Biology, 378: 1052-1063 (2008)
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    F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan, "Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms" RNA, 14: 1164-1173 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF]

    A. W. R. Serohijos, T. Hegedus, A. A. Aleksandrov, L. He, L. Cui, N. V. Dokholyan, and J. R. Riordan, "Phenylalanine 508 forms an interdomain contact in the CFTR structure crucial to folding and function" Proceedings of the National Academy of Sciences USA, 105: 3256-3261 (2008)
    [Adobe PDF][Supporting Information, Adobe PDF]

    A. W. R. Serohijos, T. Hegedus, J. R. Riordan, and N. V. Dokholyan, "Diminished self-chaperoning activity of the ΔF508 mutant CFTR results in protein misfolding" Public Library of Science Computational Biology, 4: e1000008 (2008)
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    S. Sharma, F. Ding, and N. V. Dokholyan, "Probing protein aggregation using simplified models and discrete molecular dynamics" Frontiers in Bioscience, 13: 4795-4808 (2008)
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    S. Sharma and N. V. Dokholyan, "DNA sequence mediates nucleosome structure and stability" Biophysical Journal, 94: 1-3 (2008)
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    Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, and N. V. Dokholyan, "Protein folding: then and now" Archives of Biochemistry and Biophysics, 469: 4-19 (2008)
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    S. Yin, F. Ding, and N. V. Dokholyan, "Modeling backbone flexibility improves protein stability estimation" Structure, 15: 1567-1576 (2007)
    [Adobe PDF] [Supporting Information, Adobe PDF]

    A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, H. E. Stanley, "Parallel folding pathways in the Src SH3 domain" Journal of Molecular Biology, 373: 1348-1360 (2007)
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    S. Sharma, P. Gong, B. Temple, D. Bhattacharyya, N. V. Dokholyan, and S. G. Chaney, "Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics" Journal of Molecular Biology, 373: 1123-1140 (2007)
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    S. D. Khare and N. V. Dokholyan, "Molecular mechanisms of polypeptide aggregation in human diseases" Current Protein & Peptide Science, 8: 573-579 (2007)
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    S. Barton, R. Jacak, S. D. Khare, F. Ding, and N. V. Dokholyan, "The length dependence of the polyQ-mediated protein aggregation" Journal of Biological Chemistry, 282: 25487-25492 (2007)
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    Y. Chen, S. L. Campbell, and N. V. Dokholyan, "A constraint-free method for selecting protein conformations consistent with NMR dynamics data" Biophysical Journal, 93: 2300-2306 (2007)
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    S. Yin, F. Ding, and N. V. Dokholyan, "Eris: An automated estimator of protein stability" Nature Methods, 4: 466-467 (2007)
    [Adobe PDF][Supporting Information, Adobe PDF][Portal: Eris]

    Y. Chen, F. Ding, and N. V. Dokholyan, "Fidelity of protein structure reconstruction from inter-residue proximity constraints" Journal of Physical Chemistry B, 111: 7432-7438 (2007)
    [Adobe PDF][Supporting Information, Adobe PDF]

    C. Davis, H. Nie, and N. V. Dokholyan, "Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes" Physical Review E, 75: 051921 (2007)
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    S. Sharma, F. Ding, and N. V. Dokholyan, "Multi-scale modeling of nucleosome dynamics" Biophysical Journal, 92 1457-1470 (2007)
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    B. Podobnik, J. Shao, N. V. Dokholyan, V. Zlatic, H. E. Stanley, I. Grosse, "Similarity and dissimilarity in correlations of genomic DNA" Physica A, 373: 497-502 (2007)
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    A. W. Serohijos, Y. Chen, F. Ding, T. C. Elston, and N. V. Dokholyan, “A new structural model reveals energy transduction in dynein” Proceedings of the National Academy of Sciences USA, 103: 18540-18545 (2006)
    [Adobe PDF][Supporting Information, Adobe PDF]

    E. V. Petrotchenko, D. Pasek, P. Elms, N. V. Dokholyan, G. Meissner, and C. H. Borchers, “Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins” Analytical Chemistry, 78: 7959-7966 (2006)
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    S. Sharma, F. Ding, H. Nie, D. Watson, A. Unnithan, J. Lopp, D. Pozefsky, and N. V. Dokholyan, "iFold: A platform for interactive folding simulations of proteins" Bioinformatics, 22: 2693-2694 (2006)
    [Adobe PDF][Supporting Information, Adobe PDF][Portal: iFold]

    Y. Chen and N. V. Dokholyan, "Insights into allosteric control of vinculin function from its large-scale conformational dynamics" Journal of Biological Chemistry, 281: 29148-29154 (2006)
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    S. D. Khare, M. Caplow, and N. V. Dokholyan, "FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis" Amyloid: the Journal of Protein Folding Disorders, 13: 226 - 235 (2006)
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    F. Ding and N. V. Dokholyan, "Emergence of protein fold families through rational design" Public Library of Science Computational Biology, 2: e85 (2006) [Cover article]
    [Adobe PDF][Supporting Information, Adobe PDF]

    Y. Chen and N. V. Dokholyan, "The coordinated evolution of yeast proteins constrained by functional modularity" Trends in Genetics, 22: 416-419 (2006)
    [Adobe PDF][Supporting Information, Adobe PDF]

    K. Bloom, S. Sharma, and N. V. Dokholyan, "The path of DNA in the kinetochore" Current Biology, 16: R276-R278 (2006)
    [Adobe PDF][Supporting Information, Adobe PDF]

    S. D. Khare and N. V. Dokholyan, "Common dynamical signatures of FALS-associated structurally-diverse Cu, Zn superoxide dismutase mutants" Proceedings of the National Academy of Sciences USA, 103: 3147-3152 (2006).
    [Adobe PDF][Supporting Information, Adobe PDF]

    V. V. Demidov, N. V. Dokholyan, C. Witte-Hoffman, P. Chalasani, H.-W. Yiu, F. Ding, Y. Yu, C. R. Cantor, N. E. Broude, "Fast complementation of split fluorescent protein triggered by DNA hybridization" Proceedings of the National Academy of Sciences USA, 103: 2052-2056 (2006).
    [Adobe PDF][Supporting Information, Adobe PDF]

    N. V. Dokholyan, "Studies of folding and misfolding using simplified models", Current Opinion in Structural Biology, 16: 79-85 (2006).
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    F. Ding, K. C. Prutzman, S. L. Campbell, and N. V. Dokholyan, "Topological determinants of protein domain swapping", Structure, 14: 5-14 (2006).
    [Adobe PDF][Portal: H-predictor]

    F. Ding, S. V. Buldyrev, and N. V. Dokholyan, "Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model", Biophysical Journal, 88: 147-155 (2005).
    [Adobe PDF][Supporting Information, Adobe PDF]

    N. V. Dokholyan, "The architecture of the protein domain universe" Gene, 347: 199-205 (2005); q-bio.MN/0408006.
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    F. Ding, R. K. Jha, and N. V. Dokholyan, "Scaling behavior and structure of denatured proteins", Structure, 13: 1047-1054 (2005) [Cover article].
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    F. Ding and N. V. Dokholyan, "Simple but predictive protein models", Trends in Biotechnology, 23: 450-455 (2005).
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    S. D. Khare, K. C. Wilcox, P. Gong, and N. V. Dokholyan, "Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation" Proteins: Structure, Function, and Bioinformatics, 61: 617-632 (2005).
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    F. Ding, W. Guo, N. V. Dokholyan, E. I. Shakhnovich, and J.-E. Shea, "Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations", Journal of Molecular Biology, 350: 1035-1050 (2005).
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    S. D. Khare, F. Ding, K. N. Gwanmesia, and N. V. Dokholyan, "Molecular origin of polyglutamine-mediated protein aggregation in neurodegenerative diseases", Public Library of Science Computational Biology, 1: e30 (2005) [Cover article].
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    Y. Chen and N. V. Dokholyan, "A single disulfide bond differentiates aggregation pathways of ß2-microglobulin", Journal of Molecular Biology, 354: 473-482 (2005).
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    F. Ding, J. J. LaRocque, and N. V. Dokholyan, "Direct observation of protein folding, aggregation, and a prion-like conformational conversion", Journal of Biological Chemistry, 280: 40235-40240 (2005).
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    N. V. Dokholyan, "What is the protein design alphabet?" Proteins: Structure, Function, and Bioinformatics, 54: 622-628 (2004).
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    G. Tiana, B. E. Shakhnovich, N. V. Dokholyan, and E. I. Shakhnovich, "Imprint of evolution on protein structures" Proceedings of the National Academy of Sciences USA, 101: 2846-2851 (2004).
    [Adobe PDF][Supplemental information, Adobe PDF]

    J. Khatun, S. D. Khare, and N. V. Dokholyan, "Can contact potentials reliably predict stability of proteins?" Journal of Molecular Biology, 336: 1223-1238 (2004).
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    S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz , H. E. Stanley, and N. V. Dokholyan, "Discrete molecular dynamics simulations of peptide aggregation" Physics Review E, 69: 041908 (2004); cond-mat/0312702.
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    J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, "Multiple folding pathways of the SH3 domain." Biophysical Journal, 87: 521-533 (2004).
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    G. Tiana, N. V. Dokholyan, Ricardo A. Broglia, and E. I. Shakhnovich, "The evolution dynamics of model proteins" Journal of Chemical Physics, 121: 2381-2389 (2004).
    [Adobe PDF]

    B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, "Molecular dynamics simulation of Amyloid beta dimer formation" Biophysical Journal, 87: 2310-2321 (2004).
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    S. D. Khare, M. Caplow, and N. V. Dokholyan, "The rate and equilibrium constants for a multi-step reaction sequence for the aggregation of superoxide dismutase in ALS" Proceedings of the National Academy of Sciences USA, 101: 15094-15099 (2004).
    [Adobe PDF] [Supporting Information, Adobe PDF]

    R. D. S. Dixon, Y. Chen, F. Ding, S. D. Khare, K. C. Prutzman, M. D. Schaller, S. L. Campbell, and N. V. Dokholyan, "New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate" Structure, 12: 2161-2171 (2004).
    [Adobe PDF] [Supporting Information, Adobe PDF]

    B. E. Shakhnovich, N. V. Dokholyan, C. DeLisi, and E. I. Shakhnovich, "Functional fingerprints of folds: Evidence for correlated structure-function evolution" Journal of Molecular Biology, 326: 1-9 (2003).
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    F. Ding, J. M. Borreguero, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, "A mechanism for the alpha-helix to beta-hairpin transition", Proteins: Structure, Function, and Genetics, 53: 220-228 (2003).
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    E. J. Deeds, N. V. Dokholyan, and E. I. Shakhnovich, "Protein evolution within a structural space", Biophysical Journal, 85: 2962-2972 (2003); cond-mat/0306011.
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    M. I. Marqués, J. M. Borreguero, H. E. Stanley, and N. V. Dokholyan, "Possible mechanism for cold denaturation of proteins at high pressure", Physics Review Letters, 91: 138103 (2003); also Virtual J. Biol. Phys. Res. 6 (2003); cond-mat/0212639.
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    J. Pei, N. V. Dokholyan, E. I. Shakhnovich, and N. V. Grishin, "Modeling protein evolution: protein design method and its applications." Proceedings of the National Academy of Sciences USA, 100: 11361–11366 (2003).
    [Adobe PDF][Supporting Information, Adobe PDF]

    S. D. Khare, F. Ding, and N. V. Dokholyan, "Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis" Journal of Molecular Biology, 334: 515–525 (2003); physics/0306200.
    [Adobe PDF]

    E. López, S. V. Buldyrev, N. V. Dokholyan, L. Goldmakher, S. Havlin, P. R. King, H. E. Stanley, "Postbreakthrough behavior in flow through porous media" Physics Review E, 67: 056314 (2003).
    [Adobe PDF]

    S. V. Buldyrev, N. V. Dokholyan, S. Erramilli, M. Hong, J. Y. Kim, G. Malescio, and H. E. Stanley, "Hierarchy in social organization" Physica A, 330: 659-665 (2003).
    [Adobe PDF]

    N. V. Dokholyan, E. Pitard, S. V. Buldyrev, and H. Eugene Stanley, "Glassy behavior of a homopolymer from molecular dynamics simulations." Physics Review E, 65: 030801(R) (2002); cond-mat/0109198
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    J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Thermodynamics and folding kinetics analysis of the SH3 domain from Discrete Molecular Dynamics." Journal of Molecular Biology, 318: 863-876 (2002).
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    N. V. Dokholyan, L. A. Mirny, and E. I. Shakhnovich, "Understanding conserved amino acids in proteins." Physica A, 314: 600-606 (2002); cond-mat/0007084
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    N. V. Dokholyan, L. Li, F. Ding, and E. I. Shakhnovich, "Topological determinants of protein folding." Proceedings of the National Academy of Sciences USA, 99: 8637-8641(2002).
    [Adobe PDF]

    M. Vendruscolo, N. V. Dokholyan, E. Paci and M. Karplus, "A small-world view of the amino acids that play a key role in protein folding." Physics Review E, 65: 061910 (2002).
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    N. V. Dokholyan, B. E. Shakhnovich, and E. I. Shakhnovich, "Expanding protein universe and its origin from the biological Big Bang." Proceedings of the National Academy of Sciences USA, 99: 14132-14136 (2002).
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    F. Ding, N. V. Dokholyan, S.V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Direct molecular dynamics observation of protein folding transition state ensemble." Biophysical Journal, 83: 3525-3532 (2002).
    [Adobe PDF]

    F. Ding, N. V. Dokholyan, S.V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Molecular dynamic simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism." Journal of Molecular Biology, 324: 851-857 (2002).
    [Adobe PDF]

    P. R. King, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, E. Lopez, G. Paul, H. E. Stanley, "Uncertainty in oil production predicted by percolation theory." Physica A, 306: 376-380 (2002).
    [Adobe PDF]

    P. R. King, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, E. Lopez, G. Paul, H. E. Stanley, "Using percolation theory to predict oil field performance." Physica A, 314: 103-108 (2002).
    [Adobe PDF]

    P. R. King, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, E. López, G. Paul, H. E. Stanley, "Percolation Theory." DIALOG (London Petrophysical Society Newsletter), 10(3) (2002).
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    P. R. King, S. V. Buldyrev, N. V. Dokholyan, Y. Lee, S. Havlin, G. Paul, H. E. Stanley, & N. Vandesteeg "Predicting oil recovery using percolation theory." Petroleum Geoscience, 7: S105-S107 (2001).
    [Adobe PDF]
    A. Scala, N. V. Dokholyan, S. V. Buldyrev, and H. E. Stanley, "Thermodynamically important contacts in folding of model proteins." Physics Review E, 63: 032901 (2001); cond-mat/0012288
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    N. V. Dokholyan and E. I. Shakhnovich, "Understanding hierarchical protein evolution from first principles." Journal of Molecular Biology, 312: 289-307 (2001); cond-mat/0104469.
    [Adobe PDF]
    G. Paul, S. V. Buldyrev, N. V. Dokholyan, P. R. King, Y. Lee, S. Havlin, & H. E. Stanley, "Dependence of conductance on percolation backbone mass." Physics Review E, 61: 3435-3440 (2000); cond-mat/9910236
    [Adobe PDF]
    J. S. Andrade Jr., S. V. Buldyrev, N. V. Dokholyan, S. Havlin, P. R. King, Y. Lee, G. Paul, & H. E. Stanley, "Flow in percolation clusters." Physics Review E, 62: 8270-8281 (2000); cond-mat/0004397
    [Adobe PDF]

    N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distributions of dimeric tandem repeats in noncoding and coding DNA sequences." Journal of Theoretical Biology, 202: 273-282 (2000).
    [Adobe PDF]

    N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Identifying the protein folding nucleus using molecular dynamics." Journal of Molecular Biology 296: 1183-1188 (2000); cond-mat/9812284
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    N. V. Dokholyan, "The protein folding problem." Recent Research Developments in Statistical Physics, 1: 77-84 (2000).
    [Adobe PDF]

    R. H. R. Stanley, N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Clumping of identical oligonucleotides in coding and noncoding DNA sequences." Journal of Biomolecular Structure and Dynamics, 17: 79-87 (1999).
    [Adobe PDF]

    S. V. Buldyrev, N. V. Dokholyan, S. Havlin, H. E. Stanley, and R. H. R. Stanley, "Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences." Physica A, 273: 19-32 (1999).
    [Adobe PDF]

    N. V. Dokholyan, S. V. Buldyrev, S. Havlin, P. King, Y. Lee, and H. E. Stanley, "Distribution of shortest paths in percolation." Physica A, 266: 53-59 (1999).
    [Adobe PDF]
    P. King, J. S. Andrade Jr., S. V. Buldyrev, N. V. Dokholyan, Y. Lee, S. Havlin, and H. E. Stanley, "Percolation and Oil Recovery." Physica A, 266: 107-114 (1999).
    [Adobe PDF]
    Y. Lee, J. S. Andrade Jr., S. V. Buldyrev, N. V. Dokholyan, S. Havlin, P. R. King, G. Paul, & H. E. Stanley, "Traveling time and traveling length for flow in porous media." Physics Review E, 60: 3425-3428 (1999); cond-mat/9903066
    [Adobe PDF]
    P. King, S. V. Buldyrev, N. V. Dokholyan, S. Havlin, Y. Lee, and H. E. Stanley, "Application of statistical physics to the oil industry: Predicting oil recovery using percolation theory." Physica A, 274: 60-66 (1999).
    [Adobe PDF]
    N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Molecular dynamics studies of folding of a protein-like model." Folding & Design, 3: 577-587 (1998); cond-mat/9812291
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    M. Hong, A. Jeung, N. V. Dokholyan, T. I. Smith, H. A. Schwettman, P. Huie, and S. Erramilli, "Imaging single living cells with a scanning near-field infrared microscope based on a free electron laser." Nuclear Instruments and Methods in Physics Research B, 144: 246-255, (1998).
    [Adobe PDF]

    N. V. Dokholyan, Y. Lee, S. V. Buldyrev, S. Havlin, H. E. Stanley, and P. King, "Scaling of the distribution of shortest paths in percolation." Journal of Statistical Physics, 93: 603-613 (1998); cond-mat/9908435
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    N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Model of unequal chromosomal crossing over in DNA sequences." Physica A, 249: 594-599 (1998).
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    S. V. Buldyrev, N. V. Dokholyan, A. L. Goldberger, S. Havlin, C.-K. Peng, H. E. Stanley, and G. M. Viswanathan, "Analysis of DNA sequences using methods of statistical physics." Physica A, 249: 430-438 (1998).
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    N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distribution of base pair repeats in coding and noncoding DNA sequences." Physics Review Letters, 79: 5182-5185 (1997).
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    N. V. Dokholyan, G. V. Jikia, "Single top quark production and Vtb CKM matrix element measurement in high energy e+e- collisions." Physics Letters B, 336: 251-256 (1994).
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JOURNAL ARTICLES BOOK CHAPTERS CONFERENCE PROCEEDINGS ARTICLES

    S. Yin, F. Ding, and N. V. Dokholyan, "Computational evaluation of protein stability change upon mutations using Eris." in "In Vitro Mutagenesis Protocols" Editor: J. Braman. Humana Press (2009)

    S. G. Chaney, S. Ramachandran, S. Sharma, N. V. Dokholyan, B. Temple, D. Bhattacharyya, Y. Wu and S. Campbell, "Differences in conformation and conformational dynamics between cisplatin and oxaliplatin DNA adducts." in "Platinum and Other Heavy Metal Compounds in Cancer Chemotherapy: Molecular Mechanisms and Clinical Applications (Cancer Drug Discovery and Development)" Editors: A. Bonetti, R. Leone, F. M. Muggia and S. B. Howell. pp. 157-169. Humana Press (2009)
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    N. V. Dokholyan, "Protein designability and engineering." in "Structural Bioinformatics" Editors: P. Bourne and J. Gu. John Wiley & Sons (2009)

    N. V. Dokholyan and E. I. Shakhnovich, "Towards unifying protein evolution theory." in "Structural approaches to sequence evolution: Molecules, networks, populations" Editors: U. Bastolla, M. Porto, H. E. Roman, and M. Vendruscolo, pp 113-126. Springer, Berlin (2007)
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    N. V. Dokholyan and E. I. Shakhnovich, "Scale-free evolution: from proteins to organisms." in "Power Laws, Scale-free Networks and Genome Biology" Editors: E. V. Koonin, Y. I. Wolf, and G. P. Karev, pp 86-105. Eurekah.com and Springer (2006)
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    N. V. Dokholyan, J. M. Borreguero, S. V. Buldyrev, F. Ding, H. E. Stanley, and E. I. Shakhnovich, "Identifying the importance of amino acids for protein folding from crystal structures." Methods in Enzymology Vol. 374: pp 618-640 Macromolecular crystallography D. Editors: C. W. Carter Jr. and R. M. Sweet (2003)
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JOURNAL ARTICLES BOOK CHAPTERS

CONFERENCE PROCEEDINGS ARTICLES

    N. V. Dokholyan, “Simplified approaches to complex biological systems”, Proceedings of the From Computational Biophysics to Systems Biology (CBSB08) Symposium, May 19-21, 2008. Eds. U. H. E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler, and O. Zimmermann, NIC Series, 40: 85-88 (2008).
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    N. V. Dokholyan, C. Glabe, D. Holtzman, A. Koudinov, A. Lomakin, N. Oyler, N. Paganini, D. Teplow, D. Thirumalai, and R. Tycko, “Live discussion: Protein folding and neurodegeneration: Biophysics to the rescue?”, Journal of Alzheimer’s Disease, 6: 99–105 (2004).
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    N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, "Kinetics of the protein folding transition." AIP Proceedings of the Third Tohwa University Conference on Statistical Physics, November 8-12, 1999 419-425 (2000).
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    N. V. Dokholyan and E. I. Shakhnovich, "Two models of amino acid conservation in proteins." Proceedings of the International School of Physics "Enrico Fermi" Course CXLV: "Protein folding, evolution and design", Varenna, Italy p. 227-245 (2000).


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