Kesner, B. A., Milgram, S. L., Temple, B. S. and Dokholyan, N. V. "Isoform divergence of the filamin family of proteins", Molecular Biology and Evolution, in press (2009)

Yin, S., Proctor, E. A., Lugovskoy, A. A. and Dokholyan, N. V. "Fast screening of protein surfaces using geometric invariant fingerprints", Proceedings of the National Academy of Sciences USA, 106:16622-16626 (2009)

Kota, P., Summers, D. W., Ren, H-Y., Cyr, D. M. and Dokholyan, N. V. "Identification of a consensus motif in substrates bound by a type I Hsp40", Proceedings of the National Academy of Sciences USA, 106:11073-11078 (2009)

Kesner, B. A., Ding, F., Temple, B. S., and Dokholyan, N. V. "N-terminal strands of filamin Ig domains act as a conformational switch under biological forces", Proteins: Structure, Function, and Bioinformatics, in press (2009)

Serohijos, A. W. R., Tsygankov, D., Liu, S., Elston, T. C., and Dokholyan, N. V. "Multiscale approaches for studying energy transduction in dynein", Physical Chemistry Chemical Physics, 11:4840-4850 (2009)

Wilcox, K. C., Zhou, L., Jordon, J., Huang, Y., Yu, Y., Redler, R. L., Chen, X., Caplow, M., and Dokholyan, N. V. "Modifications of SOD1 in human erythrocytes: A possible role in ALS", Journal of Biological Chemistry, 284:13940-13947 (2009)

Ramachandran, S., Serohijos, A. W. R., Xu, L., Meissner, G., and Dokholyan, N. V., "Ryanodine receptor pore structure and function", Public Library of Science Computational Biology, 5:e1000367 (2009)

Torres, M. P., Lee, M. J., Ding, F., Purbeck, C., Kuhlman, B., Dokholyan, N. V., and Dohlman, H. G., "G protein mono-ubiquitination by the RSP5 ubiquitin ligase", Journal of Biological Chemistry, 284:8940-8950 (2009)

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

Gherghe, C. M., Leonard, C. W., Ding, F., Dokholyan, N. V., and Weeks, K. M., "Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics", Journal of the American Chemical Society, 131:2541-2546 (2009)

Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H. M., Jones, B., Brenner, S., Burley, S. K., Das, R., Dokholyan, N. V., Dunbrack, R. L. Jr., Fidelis, K., Fiser, A., Godzik, A., Humblet, C., Jacobson, M. P., Joachimiak, A., Krystek, S., Kortemme, T., Kryshtafovych, A., Montelione, G., Moult, J., Murray, D., Sanchez, R., Sosnick, T. R., Standley, D. M., Stouch, T., Vajda, S., Westbrook, J. D., and Wilson, I. A., "Outcome of a workshop on applications of protein models in biomedical research", Structure, 17:151-159 (2009)

Tsygankov, D., Serohijos, A. W. R., Dokholyan, N. V., and Elston, T. C., "Kinetic models for the coordinated stepping of cytoplasmic dynein", Journal of Chemical Physics, 130:25101 (2009)

Meissner, G., Pasek, D. A., Yamaguchi, N., Ramachandran, S., Dokholyan, N. V., and Tripathy, A., "Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels", Proteins: Structure, Function, and Bioinformatics, 74:207-211 (2009)

Petrotchenko, E. V., Xiao, K., Cable, J., Chen, Y., Dokholyan, N. V., and Borchers, C. H., "Bimane Bisthiopropionic Acid N-Succinimidyl Ester (BiPS), a photo-cleavable, isotopically-coded, fluorescent crosslinker for structural proteomics", Molecular and Cellular Proteomics, 8:273-286 (2009)

Ding, F., and Dokholyan, N. V., "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)

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

Ozvegy-Laczka, C., Laczko, R., Hegedus, C., Litman, T., Varady, G., Goda, K., Hegedus, T. Z., Dokholyan, N. V., Sorrentino, B. P., Varadi, A., Sarkadi, B., "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)

Yin, S., Biedermannova, L., Vondrasek, J., and Dokholyan, N. V., "MedusaScore: An accurate force-field based scoring function for virtual drug screening", Journal of Chemical Information and Modeling, 48:1656-1662 (2008)

Sharma, S., Ding, F., and Dokholyan, N. V., "iFoldRNA: Three-dimensional RNA structure prediction and folding", Bioinformatics, 24:1951-1952 (2008)

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

Chen, Y., and Dokholyan, N. V., "Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly and worm", Molecular Biology and Evolution, 25:1530-1533 (2008)

Teotico, D. G., Frazier, M. L., Ding, F., Dokholyan, N. V., Temple, B. R. S., and Redinbo, M. R., "Active nuclear receptors exhibit highly correlated AF-2 domain motions", Public Library of Science Computational Biology, 4:e1000111 (2008)

Ding, F., Tsao, D., Nie, H., and Dokholyan, N. V., "Ab initio folding of proteins with all-atom discrete molecular dynamics", Structure, 16:1010-1018 (2008)

Hegedus, T. Z., Serohijos, A. W. R., Dokholyan, N. V., He, L., and Riordan, J. R., "Computational studies reveal phosphorylation dependent changes in the unstructured R domain of CFTR", Journal of Molecular Biology, 378:1052-1063 (2008)

Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E., and Dokholyan, N. V., "Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms", RNA, 14:1164-1173 (2008)

Serohijos, A. W. R., Hegedus, T., Aleksandrov, A. A., He, L., Cui, L., Dokholyan, N. V., and Riordan, J. R., "Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function", Proceedings of the National Academy of Sciences USA, 105:3256-3261 (2008)

Serohijos, A. W. R., Hegedus, T., Riordan, J. R., and Dokholyan, N. V., "Diminished self-chaperoning activity of the ΔF508 mutant CFTR results in protein misfolding", Public Library of Science Computational Biology, 4:e1000008 (2008)

Sharma, S., and Dokholyan, N. V., "DNA sequence mediates nucleosome structure and stability", Biophysical Journal, 94:1-3 (2008)

Chen, Y., Ding, F., Nie, H., Serohijos, A. W., Sharma, S., Wilcox, K. C., Yin, S., and Dokholyan, N. V., "Protein folding: then and now", Archives of Biochemistry and Biophysics, 469:4-19 (2008)

Sharma, S., Ding, F., and Dokholyan, N. V., "Probing protein aggregation using discrete molecular dynamics", Frontier in Bioscience, 13:4795-4808 (2008)

Yin, S., Ding, F., and Dokholyan, N. V., "Modeling backbone flexibility improves protein stability estimation", Structure, 15:1567-1576 (2007)

Lam, A. R., Borreguero, J. M., Ding, F., Dokholyan, N. V., Buldyrev, S. V., Shakhnovich, E. I., and Stanley, H. E., "Parallel folding pathways in the SH3 domain protein", Journal of Molecular Biology, 373:1348-1360 (2007)

Sharma, S., Gong, P., Temple, B., Bhattacharyya, D., Dokholyan, N. V., and Chaney, S. G., "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)

Khare, S. D., and Dokholyan, N. V., "Molecular mechanisms of polypeptide aggregation in human diseases", Current Protein & Peptide Science, 8:573-579 (2007)

Barton, S., Jacak, R., Khare, S. D., Ding, F., and Dokholyan, N. V., "The length dependence of the polyQ-mediated protein aggregation", Journal of Biological Chemistry, 282:25487-25492 (2007)

Chen, Y., Campbell, S. L., and Dokholyan, N. V., "Deciphering protein dynamics from NMR data using explicit structure sampling and selection", Biophysical Journal, 93:2300-2306 (2007)

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

Yin, S., Ding, F., and Dokholyan, N. V., "Eris: An automated estimator of protein stability", Nature Methods, 4:466-467 (2007)

Davis, C. H., Nie, H., and Dokholyan, N. V., "Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes", Physical Review E, 75:51921 (2007)

Podobnik, B., Shao, J., Dokholyan, N. V., Zlatic, V., Stanley, H. E., and Grosse, I., "Similarity and dissimilarity in correlations of genomic DNA", Physica A, 373:497-502 (2007)

Sharma, S., Ding, F., and Dokholyan, N. V., "Multi-scale modeling of nucleosome dynamics", Biophysical Journal, 92:1457-1470 (2007)

Serohijos, A. W., Chen, Y., Ding, F., Elston, T. C., and Dokholyan, N. V., "A structural model reveals energy transduction in dynein", Proceedings of the National Academy of Sciences USA, 103:18540-18545 (2006)

Petrotchenko, E. V., Pasek, D., Elms, P., Dokholyan, N. V., Meissner, G., and Borchers, C. H., "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)

Sharma, S., Ding, F., Nie, H., Watson, D., Unnithan, A., Lopp, J., Pozefsky, D., and Dokholyan, N. V., "iFold: A platform for interactive folding simulations of proteins", Bioinformatics, 22:2693-2694 (2006)

Chen, Y., and Dokholyan, N. V., "Insights into allosteric control of vinculin function from its large-scale conformational dynamics", Journal of Biological Chemistry, 281:29148-29154 (2006)

Khare, S. D., Caplow, M., and Dokholyan, N. V., "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)

Ding, F., and Dokholyan, N. V., "Emergence of protein fold families through rational design", Public Library of Science Computational Biology, 2:e85 (2006)

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

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

Khare, S. D., and Dokholyan, N. V., "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)

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

Dokholyan, N. V., "Studies of folding and misfolding using simplified models", Current Opinions in Structural Biology, 16:79-85 (2006)

Ding, F., Prutzman, K. C., Campbell, S. L., and Dokholyan, N. V., "Topological determinants of protein domain swapping", Structure, 14:5-14 (2006)

Ding, F., Larocque, J. J., and Dokholyan, N. V., "Direct observation of protein folding, aggregation, and a prion-like conformational conversion", Journal of Biological Chemistry, 280:40235-40240 (2005)

Chen, Y., and Dokholyan, N. V., "A single disulfide bond differentiates aggregation pathways of β2-microglobulin", Journal of Molecular Biology, 354:473-482 (2005)

Khare, S. D., Ding, F., Gwanmesia, K. N., and Dokholyan, N. V., "Molecular origin of polyglutamine-mediated protein aggregation in neurodegenerative diseases", Public Library of Science Computational Biology, 1:e30 (2005)

Ding, F., Guo, W. H., Dokholyan, N. V., Shakhnovich, E. I., and Shea, J.-E., "Reconstruction of src SH3 transition state ensemble using multiscale molecular dynamics simulations", Journal of Molecular Biology, 350:1035-1050 (2005)

Khare, S. D., Wilcox, K. C., Gong, P., and Dokholyan, N. V., "Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation", Proteins: Structure, Function, and Bioinformatics, 61:617-632 (2005)

Ding, F., and Dokholyan, N. V., "Simple but predictive protein models", Trends in Biotechnology, 23:450-455 (2005)

Ding, F., Jha, R. K., and Dokholyan, N. V., "Scaling behavior and structure of denatured proteins", Structure, 13:1047-1054 (2005)

Dokholyan, N. V., "The architecture of the protein domain universe", Gene, 347:199-205 (2005)

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

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

Khare, S. D., Caplow, M., and Dokholyan, N. V., "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)

Urbanc, B., Cruz, L., Ding, F., Sammond, D., Khare, S. D., Buldyrev, S. V., Stanley, H. E., and Dokholyan, N. V., "Molecular dynamics simulation of Amyloid beta dimer formation", Biophysical Journal, 87:2310-2321 (2004)

Tiana, G., Dokholyan, N. V., Broglia, R. A., and Shakhnovich, E. I., "The evolution dynamics of model proteins", Journal of Chemical Physics, 121:2381-2389 (2004)

Borreguero, J. M., Ding, F., Buldyrev, S. V., Stanley, H. E., and Dokholyan, N. V., "Multiple folding pathways of the SH3 domain", Biophysical Journal, 87:521-533 (2004)

Peng, S., Ding, F., Urbanc, B., Buldyrev, S. V., Cruz, L., Stanley, H. E., and Dokholyan, N. V., "Discrete molecular dynamics simulations of peptide aggregation", Physical Review E, 69:41908 (2004)

Khatun, J., Khare, S. D., and Dokholyan, N. V., "Can contact potentials reliably predict stability of proteins?", Journal of Molecular Biology, 336:1223-1238 (2004)

Tiana, G., Shakhnovich, B. E., Dokholyan, N. V., and Shakhnovich, E. I., "Imprint of evolution on protein structures", Proceedings of the National Academy of Sciences USA, 101:2846-2851 (2004)

Dokholyan, N. V., "What is the protein design alphabet?", Proteins: Structure, Function, and Bioinformatics, 54:622-628 (2004)

Khare, S. D., Ding, F., and Dokholyan, N. V., "Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis", Journal of Molecular Biology, 334:515-525 (2003)

Pei, J., Dokholyan, N. V., Shakhnovich, E. I., and Grishin, N. V., "Using protein design for homology detection and active site searches", Proceedings of the National Academy of Sciences USA, 100:11361-11366 (2003)

Marques, M. I., Borreguero, J. M., Stanley, H. E., and Dokholyan, N. V., "Possible mechanism for cold denaturation of proteins at high pressure", Physical Review Letters, 91:138103 (2003)

Deeds, E. J., Dokholyan, N. V., and Shakhnovich, E. I., "Protein evolution within a structural space", Biophysical Journal, 85:2962-2972 (2003)

Ding, F., Borreguero, J. M., Buldyrev, S. V., Stanley, H. E., and Dokholyan, N. V., "Mechanism for the α-Helix to β-Hairpin Transition", Proteins: Structure, Function, and Genetics, 53:220-228 (2003)

Shakhnovich, B. E., Dokholyan, N. V., DeLisi, C., and Shakhnovich, E. I., "Functional fingerprints of folds: Evidence for correlated structure-function evolution", Journal of Molecular Biology, 326:1-9 (2003)

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

Lopez, E., Buldyrev, S. V., Dokholyan, N. V., Goldmakher, L., Havlin, S., King, P. R., and Stanley, H. E., "Postbreakthrough behavior in flow through porous media", Physical Review E, 67:56314 (2003)

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

Ding, F., Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E., and Shakhnovich, E. I., "Direct molecular dynamics observation of protein folding transition state ensemble", Biophysical Journal, 83:3525-3532 (2002)

Dokholyan, N. V., Shakhnovich, B. E., and Shakhnovich, E. I., "Expanding protein universe and its origin from the biological Big Bang", Proceedings of the National Academy of Sciences USA, 99:-14136 (2002)

Vendruscolo, M., Dokholyan, N. V., Paci, E., and Karplus, M., "A small-world view of the amino acids that play a key role in protein folding", Physical Review E, 65:61910 (2002)

Dokholyan, N. V., Li, L., Ding, F., and Shakhnovich, E. I., "Topological determinants of protein folding", Proceedings of the National Academy of Sciences USA, 99:8637-8641 (2002)

Dokholyan, N. V., Mirny, L. A., and Shakhnovich, E. I., "Understanding conserved amino acids in proteins", Physica A, 314:600-606 (2002)

Borreguero, J. M., Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E., and Shakhnovich, E. I., "Thermodynamics and folding kinetics analysis of the SH3 domain from Discrete Molecular Dynamics", Journal of Molecular Biology, 318:863-876 (2002)

Dokholyan, N. V., Pitard, E., Buldyrev, S. V., and Stanley, H. E., "Glassy behavior of a homopolymer from molecular dynamics simulations", Physical Review E, 65:030801(R) (2002)

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

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

Dokholyan, N. V., and Shakhnovich, E. I., "Understanding hierarchical protein evolution from first principles", Journal of Molecular Biology, 312:289-307 (2001)

Scala, A., Dokholyan, N. V., Buldyrev, S. V., and Stanley, H. E., "Thermodynamically important contacts in folding of model proteins", Physical Review E, 63:32901 (2001)

King, P. R., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., Lee, Y., Paul, G., Stanley, H. E., and Vandesteeg, N., "Predicting oil recovery using percolation theory", Petroleum Geoscience, 7:S105-S107 (2001)

Dokholyan, N. V., "The protein folding problem", Recent Research Developments in Statistical Physics, 1:77-84 (2000)

Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E., and Shakhnovich, E. I., "Identifying the protein folding nucleus using molecular dynamics", Journal of Molecular Biology, 296:1183-1188 (2000)

Andrade, J. S. Jr., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., King, P. R., Lee, Y., Paul, G., and Stanley, H. E., "Flow between two sites on a percolation cluster", Physical Review E, 62:8270-8281 (2000)

Paul, G., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., King, P. R., Lee, Y., and Stanley, H. E., "Dependence of conductance on percolation backbone mass", Physical Review E, 61:3435-3440 (2000)

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

King, P. R., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., Lee, Y., Paul, G., and Stanley, H. E., "Application of statistical physics to the oil industry: Predicting oil recovery using percolation theory", Physica A, 274:60-66 (1999)

Lee, Y., Andrade, J. S. Jr., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., King, P. R., Paul, G., and Stanley, H. E., "Traveling time and traveling length in critical percolation clusters", Physical Review E, 60:3425-3428 (1999)

King, P. R., Andrade, J. S. Jr., Buldyrev, S. V., Dokholyan, N. V., Lee, Y., Havlin, S., and Stanley, H. E., "Percolation and oil recovery", Physica A, 266:107-114 (1999)

Dokholyan, N. V., Buldyrev, S. V., Havlin, S., King, P. R., Lee, Y., and Stanley, H. E., "Distribution of shortest paths in percolation", Physica A, 266:53-59 (1999)

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

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

Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E., and Shakhnovich, E. I., "Molecular dynamics studies of folding of a protein-like model", Folding and Design, 3:577-587 (1998)

Dokholyan, N. V., Lee, Y., Buldyrev, S. V., Havlin, S., King, P. R., and Stanley, H. E., "Scaling of the distribution of shortest paths in percolation", Journal of Statistical Physics, 93:603-613 (1999)

Hong, M. K., Jeung, A. G., Dokholyan, N. V., Smith, T. I., Schwettman, H. A., Huie, P., and Erramilli, S., "Imaging single living cells with a scanning near-field infrared microscope based on a free electron laser", Nuclear Instruments and Methods in Physics Research, 0:246-255 (1999)

Buldyrev, S. V., Dokholyan, N. V., Goldberger, A. L., Havlin, S., Peng, C.-K., Stanley, H. E., and Viswanathan, G. M., "Analysis of DNA sequences using methods of statistical physics", Physica A, 249:430-438 (1998)

Dokholyan, N. V., Buldyrev, S. V., Havlin, S., and Stanley, H. E., "Model of unequal chromosomal crossing over in DNA sequences", Physica A, 249:594-599 (1998)

Dokholyan, N. V., Buldyrev, S. V., Havlin, S., and Stanley, H. E., "Distribution of base pair repeats in coding and noncoding DNA sequences", Physical Review Letters, 79:5182-5185 (1997)

Dokholyan, N. V., and Jikia, G. V., "Single top quark production and V_tb CKM matrix element measurement in high energy e⁺e^- collisions", Physics Letters B, 336:251-256 (1994)

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

Yin, S., Ding, F. and Dokholyan, N. V. "Modeling mutations in proteins using Medusa and discrete molecular dynamics" in "Protein Structure Prediction: Method and Algorithms", in press, Editors: Rangwala, H. and Karypis, G. Wiley & Sons, (2009)

Chaney, S. G., Ramachandran, S., Sharma, S., Dokholyan, N. V., Temple, B., Bhattacharyya, D., Wu, Y., and Campbell, S., "Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts" in "Platinum and Other Heavy Metal Compounds in Cancer Chemotherapy", pp 157-169, Cancer Drug Discovery and Development, Editors: Bonetti, A., Leone, R., Muggia, F. M., and Howell, S. B., Humana Press, (2009)

Dokholyan, N. V., "Protein designability and engineering" in "Structural Bioinformatics", pp 961-982, Editors: Bourne. P., and Gu, J., Wiley & Sons, (2008)

Dokholyan, N. V., and Shakhnovich, E. I., "Towards unifying protein evolution theory" in "Structural approaches to sequence evolution: Molecules, networks, populations", pp 113-126, Biological and Medical Physics, Biomedical Engineering, Editors: Bastolla, U., Porto, M., Roman, H. E., and Vendruscolo, M., Springer, (2007)

Dokholyan, N. V., and Shakhnovich, E. I., "Scale-free evolution: from proteins to organisms" in "Power Laws, Scale-free Networks and Genome Biology", pp 86-105, Molecular Biology Intelligence Unit, Editors: Koonin, E. V., Wolf, Y. I., and Karev, G. P., Eurekah.com and Springer, (2006)

Dokholyan, N. V., Borreguero, J. M., Buldyrev, S. V., Ding, F., Stanley, H. E., and Shakhnovich, E. I., "Identifying importance of amino acids for protein folding from crystal structures" in "Methods in Enzymology", Vol. 374:pp 618-640, Macromolecular Crystallography D, Editors: Carter Jr. C. W., and Sweet, R. M., Elsevier, (2003)

Dokholyan, N. V., and Shakhnovich, E. I. "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, 227-245, (2000)

Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E., and Shakhnovich, E. I. "Kinetics of the protein folding transition.", AIP Proceedings of the Third Tohwa University Conference on Statistical Physics, November 8-12, 1999, 419-425, (2000)

Dokholyan, N. V., Glabe, C., Holtzman, D., Koudinov, A., Lomakin, A., Oyler, N., Paganini, N., Teplow, D., Thirumalai, D., and Tycko, R. "Live discussion: Protein folding and neurodegeneration: Biophysics to the rescue?", Journal of Alzheimer's Disease, 6:99-105, (2004)

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