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Research Output 1994 2020

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1994
11 Citations (Scopus)

Single top quark production and Vb CKM matrix element measurement in high energy e+e- collisions

Dokholyan, N. V. & Jikia, G. V., Sep 22 1994, In : Physics Letters B. 336, 2, p. 251-256 6 p.

Research output: Contribution to journalArticle

quarks
collisions
matrices
energy
1997
33 Citations (Scopus)

Distribution of base pair repeats in coding and noncoding DNA sequences

Nikolay, D. V., Sergey, B. V., Shlomo, H. & Eugene, S. H., Jan 1 1997, In : Physical Review Letters. 79, 25, p. 5182-5185 4 p.

Research output: Contribution to journalArticle

coding
deoxyribonucleic acid
dimers
distribution functions
Markov processes
1998
131 Citations (Scopus)

Analysis of DNA sequences using methods of statistical physics

Buldyrev, S. V., Dokholyan, N., Goldberger, A. L., Havlin, S., Peng, C. K., Stanley, H. E. & Viswanathan, G. M., Jan 2 1998, In : Physica A: Statistical Mechanics and its Applications. 249, 1-4, p. 430-438 9 p.

Research output: Contribution to journalArticle

Statistical Physics
DNA Sequence
deoxyribonucleic acid
Coding
Molecular Evolution
231 Citations (Scopus)

Discrete molecular dynamics studies of the folding of a protein-like model

Dokholyan, N., Buldyrev, S. V., Stanley, H. E. & Shakhnovich, E. I., Jan 1 1998, In : Folding and Design. 3, 6, p. 577-587 11 p.

Research output: Contribution to journalArticle

Protein Folding
Molecular Dynamics Simulation
Molecular dynamics
Proteins
Thermodynamics
40 Citations (Scopus)

Imaging single living cells with a scanning near-field infrared microscope based on a free electron laser

Hong, M. K., Jeung, A. G., Dokholyan, N. V., Smith, T. I., Schwettman, H. A., Huie, P. & Erramilli, S., Sep 2 1998, In : Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms. 144, 1-4, p. 246-255 10 p.

Research output: Contribution to journalArticle

Free electron lasers
free electron lasers
Lipids
lipids
near fields
13 Citations (Scopus)

Model of unequal chromosomal crossing over in DNA sequences

Dokholyan, N., Buldyrev, S. V., Havlin, S. & Stanley, H. E., Jan 2 1998, In : Physica A: Statistical Mechanics and its Applications. 249, 1-4, p. 594-599 6 p.

Research output: Contribution to journalArticle

Unequal
DNA Sequence
Distribution Function
deoxyribonucleic acid
distribution functions
50 Citations (Scopus)

Scaling of the distribution of shortest paths in percolation

Dokholyan, N., Lee, Y., Buldyrev, S. V., Havlin, S., King, P. R. & Stanley, H. E., Nov 1 1998, In : Journal of Statistical Physics. 93, 3-4, p. 603-613 11 p.

Research output: Contribution to journalArticle

Shortest path
Scaling
scaling
Distribution Function
distribution functions
1999
7 Citations (Scopus)

Clustering of identical oligomers in coding and noncoding dna sequences

Stanley, R. H. R., Dokholyan, N. V., Buldyrev, S. V., Havlin, S. & Stanley, H. E., Aug 1999, In : Journal of Biomolecular Structure and Dynamics. 17, 1, p. 79-87 9 p.

Research output: Contribution to journalArticle

Cluster Analysis
DNA
Invertebrates
Primates
Nucleic Acid Databases
78 Citations (Scopus)

Traveling time and traveling length in critical percolation clusters

Lee, Y., Andrade, J. S., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., King, P. R., Paul, G. & Stanley, H. E., Jan 1 1999, In : Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60, 3, p. 3425-3428 4 p.

Research output: Contribution to journalArticle

Probable
tracers
scaling
Scaling Relations
Euclidean Distance
2000
14 Citations (Scopus)

Dependence of conductance on percolation backbone mass

Paul, G., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., King, P. R., Lee, Y. & Eugene Stanley, H., Jan 1 2000, In : Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 61, 4, p. 3435-3440 6 p.

Research output: Contribution to journalArticle

Conductance
Backbone
Percolation Threshold
Sierpinski Gasket
Decrease
31 Citations (Scopus)

Distributions of dimeric tandem repeats in non-coding and coding DNA sequences

Dokholyan, N. V., Buldyrev, S. V., Havlin, S. & Stanley, H. E., Feb 21 2000, In : Journal of Theoretical Biology. 202, 4, p. 273-282 10 p.

Research output: Contribution to journalArticle

Tandem Repeat Sequences
tandem repeat sequences
DNA sequences
intergenic DNA
DNA Sequence
65 Citations (Scopus)

Flow between two sites on a percolation cluster

Andrade, J. S., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., King, P. R., Lee, Y., Paul, G. & Stanley, H. E., Dec 1 2000, In : Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 62, 6 B, p. 8270-8281 12 p.

Research output: Contribution to journalArticle

Porous Media
Distribution Function
distribution functions
scaling
Percolation Theory
126 Citations (Scopus)

Identifying the protein folding nucleus using molecular dynamics

Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E. & Shakhnovich, E. I., Mar 10 2000, In : Journal of Molecular Biology. 296, 5, p. 1183-1188 6 p.

Research output: Contribution to journalArticle

Protein Folding
Molecular Dynamics Simulation
Molecular Evolution
Foot
Proteins
2001
2 Citations (Scopus)

Applications of statistical physics to the oil industry: Predicting oil recovery using percolation theory

King, P. R., Buldyrev, S. V., Dokholyan, N. V., Havlin, S., Lee, Y., Paul, G., Stanley, H. E. & Vandesteeg, N., Jan 1 2001, In : Petroleum Geoscience. 7, p. S105-S117

Research output: Contribution to journalArticle

Scaling laws
Oil fields
oil industry
oil field
aid
28 Citations (Scopus)

Predicting oil recovery using percolation theory

King, P. R., Buldyrev, S. V., Dokholyan, N., Havlin, S., Lee, Y., Paul, G., Stanley, H. E. & Vandesteeg, N., Jun 27 2001, In : Petroleum Geoscience. 7, SPECIL ISSUE

Research output: Contribution to journalArticle

Scaling laws
Oil fields
oil field
aid
Oils
6 Citations (Scopus)

Thermodynamically important contacts in folding of model proteins

Scala, A., Dokholyan, N. N., Buldyrev, S. S. & Stanley, E. E., Jan 1 2001, In : Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 63, 3

Research output: Contribution to journalArticle

Folding
folding
specific heat
Contact
proteins
129 Citations (Scopus)

Understanding hierarchical protein evolution from first principles

Dokholyan, N. V. & Shakhnovich, E. I., Sep 7 2001, In : Journal of Molecular Biology. 312, 1, p. 289-307 19 p.

Research output: Contribution to journalArticle

Proteins
Amino Acids
Mutation
2002
114 Citations (Scopus)

Direct molecular dynamics observation of protein folding transition state ensemble

Ding, F., Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E. & Shakhnovich, E. I., Dec 1 2002, In : Biophysical journal. 83, 6, p. 3525-3532 8 p.

Research output: Contribution to journalArticle

Protein Folding
Molecular Dynamics Simulation
Observation
Protein Engineering
Proteins
137 Citations (Scopus)

Expanding protein universe and its origin from the biological Big Bang

Dokholyan, N. V., Shakhnovich, B. & Shakhnovich, E. I., Oct 29 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 22, p. 14132-14136 5 p.

Research output: Contribution to journalArticle

Proteins
Molecular Evolution
Origin of Life
8 Citations (Scopus)

Glassy behavior of a homopolymer from molecular dynamics simulations

Dokholyan, N. V., Pitard, E., Buldyrev, S. V. & Stanley, H. E., Mar 1 2002, In : Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 65, 3, p. 030801/1-030801/4 030801.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
molecular dynamics
Structure Factor
Polymers
simulation
131 Citations (Scopus)

Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism

Ding, F., Dokholyan, N. V., Buldyrev, S. V., Stanley, H. E. & Shakhnovich, E. I., Jan 1 2002, In : Journal of Molecular Biology. 324, 4, p. 851-857 7 p.

Research output: Contribution to journalArticle

src Homology Domains
Molecular Dynamics Simulation
Proteins
Amyloid
Hydrogen
260 Citations (Scopus)

Small-world view of the amino acids that play a key role in protein folding

Vendruscolo, M., Dokholyan, N. V., Paci, E. & Karplus, M., Jun 1 2002, In : Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 65, 6, p. 061910/1-061910/4 061910.

Research output: Contribution to journalArticle

Protein Folding
Small World
folding
amino acids
Amino Acids
50 Citations (Scopus)

Thermodynamics and folding kinetics analysis of the SH3 domain from discrete molecular dynamics

Borreguero, J. M., Dokholyan, N. V., Buldyrev, S. V., Shakhnovich, E. I. & Eugene Stanley, H., Jan 1 2002, In : Journal of Molecular Biology. 318, 3, p. 863-876 14 p.

Research output: Contribution to journalArticle

src Homology Domains
Molecular Dynamics Simulation
Thermodynamics
Proteins
Amino Acids
223 Citations (Scopus)

Topological determinants of protein folding

Dokholyan, N. V., Li, L., Ding, F. & Shakhnovich, E. I., Jun 25 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 13, p. 8637-8641 5 p.

Research output: Contribution to journalArticle

Protein Folding
Protein Conformation
Proteins
Protein C
12 Citations (Scopus)

Understanding conserved amino acids in proteins

Dokholyan, N., Mirny, L. A. & Shakhnovich, E. I., Dec 1 2002, In : Physica A: Statistical Mechanics and its Applications. 314, 1-4, p. 600-606 7 p.

Research output: Contribution to journalArticle

amino acids
Amino Acids
proteins
Protein
Physical property
14 Citations (Scopus)

Using percolation theory to predict oil field performance

King, P. R., Buldyrev, S. V., Dokholyan, N., Havlin, S., Lopez, E., Paul, G. & Stanley, H. E., Dec 1 2002, In : Physica A: Statistical Mechanics and its Applications. 314, 1-4, p. 103-108 6 p.

Research output: Contribution to journalArticle

Percolation Theory
oil fields
decision making
scaling laws
estimating
2003
55 Citations (Scopus)

Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis

Khare, S. D., Ding, F. & Dokholyan, N. V., Nov 28 2003, In : Journal of Molecular Biology. 334, 3, p. 515-525 11 p.

Research output: Contribution to journalArticle

Amyotrophic Lateral Sclerosis
Thermodynamics
Molecular Dynamics Simulation
Disulfides
Neurodegenerative Diseases
43 Citations (Scopus)

Functional fingerprints of folds: Evidence for correlated structure-function evolution

Shakhnovich, B. E., Dokholyan, N., DeLisi, C. & Shakhnovich, E. I., Feb 7 2003, In : Journal of Molecular Biology. 326, 1, p. 1-9 9 p.

Research output: Contribution to journalArticle

Dermatoglyphics
Cluster Analysis
Gene Ontology
Lenses
Protein Domains
23 Citations (Scopus)

Hierarchy in social organization

Buldyrev, S. V., Dokholyan, N., Erramilli, S., Hong, M., Kim, J. Y., Malescio, G. & Stanley, H. E., Dec 15 2003, In : Physica A: Statistical Mechanics and its Applications. 330, 3-4, p. 653-659 7 p.

Research output: Contribution to journalArticle

hierarchies
Escherichia Coli
Partitioning
Power Law
Exponent
18 Citations (Scopus)

Identifying Importance of Amino Acids for Protein Folding from Crystal Structures

Dokholyan, N., Borreguero, J. M., Buldyrev, S. V., Ding, F., Stanley, H. E. & Shakhnovich, E. I., Jan 1 2003, In : Methods in enzymology. 374, p. 616-638 23 p.

Research output: Contribution to journalArticle

Protein Folding
Amino Acids
182 Citations (Scopus)

Mechanism for the α-helix to β-hairpin transition

Ding, F., Borreguero, J. M., Buldyrey, S. V., Stanley, H. E. & Dokholyan, N. V., Nov 1 2003, In : Proteins: Structure, Function and Genetics. 53, 2, p. 220-228 9 p.

Research output: Contribution to journalArticle

Agglomeration
Hydrogen
Hydrogen bonds
Peptides
Proteins
81 Citations (Scopus)

Possible mechanism for cold denaturation of proteins at high pressure

Marqués, M. I., Borreguero, J. M., Stanley, H. E. & Dokholyan, N. V., Jan 1 2003, In : Physical Review Letters. 91, 13

Research output: Contribution to journalArticle

biopolymer denaturation
proteins
water
water pressure
baths
18 Citations (Scopus)

Postbreakthrough behavior in flow through porous media

López, E., Buldyrev, S. V., Dokholyan, N., Goldmakher, L., Havlin, S., King, P. R. & Stanely, H. E., May 1 2003, In : Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 67, 5 2, 056314.

Research output: Contribution to journalArticle

Porous Media
Probability Distribution
occupation
pumping
2 Citations (Scopus)

Postbreakthrough behavior in flow through porous media

López, E., Buldyrev, S. V., Dokholyan, N. V., Goldmakher, L., Havlin, S., King, P. R. & Stanley, H. E., Jan 1 2003, In : Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 67, 5, 1 p.

Research output: Contribution to journalArticle

Porous Media
Power Law
Probability Density
Probability Distribution
oil recovery
27 Citations (Scopus)

Protein Evolution within a Structural Space

Deeds, E. J., Dokholyan, N. V. & Shakhnovich, E. I., Nov 2003, In : Biophysical journal. 85, 5, p. 2962-2972 11 p.

Research output: Contribution to journalArticle

Proteins
Space Simulation
Molecular Evolution
Polymers
26 Citations (Scopus)

Using protein design for homology detection and active site searches

Pei, J., Dokholyan, N. V., Shakhnovich, E. I. & Grishin, N. V., Sep 30 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 20, p. 11361-11366 6 p.

Research output: Contribution to journalArticle

Catalytic Domain
Amino Acid Substitution
Proteins
Patient Selection
2004
58 Citations (Scopus)

Can Contact Potentials Reliably Predict Stability of Proteins?

Khatun, J., Khare, S. D. & Dokholyan, N. V., Mar 5 2004, In : Journal of Molecular Biology. 336, 5, p. 1223-1238 16 p.

Research output: Contribution to journalArticle

Protein Stability
Proteins
Amino Acids
Mutation
Protein Engineering
63 Citations (Scopus)

Discrete molecular dynamics simulations of peptide aggregation

Peng, S., Ding, F., Urbanc, B., Buldyrev, S. V., Cruz, L., Stanley, H. E. & Dokholyan, N., Jan 1 2004, In : Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 69, 4 1, 041908.

Research output: Contribution to journalArticle

Discrete Dynamics
Peptides
Molecular Dynamics Simulation
peptides
Aggregation
2 Citations (Scopus)

Discrete molecular dynamics simulations of peptide aggregation

Peng, S., Ding, F., Urbanc, B., Buldyrev, S. V., Cruz, L., Stanley, H. E. & Dokholyan, N. V., Jan 1 2004, In : Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 69, 4, 1 p.

Research output: Contribution to journalArticle

Discrete Dynamics
Peptides
Molecular Dynamics Simulation
peptides
Aggregation
44 Citations (Scopus)

Imprint of evolution on protein structures

Tiana, G., Shakhnovicht, B. E., Dokholyan, N. V. & Shakhnovich, E. I., Mar 2 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 9, p. 2846-2851 6 p.

Research output: Contribution to journalArticle

Proteins
Thermodynamics
Point Mutation
Seeds
Genes
153 Citations (Scopus)

Molecular dynamics simulation of amyloid β dimer formation

Urbanc, B., Cruz, L., Ding, F., Sammond, D., Khare, S., Buldyrev, S. V., Stanley, H. E. & Dokholyan, N. V., Oct 2004, In : Biophysical journal. 87, 4, p. 2310-2321 12 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Mechanics
Amyloid
Peptides
Poisons
36 Citations (Scopus)

Multiple folding pathways of the SH3 domain

Borreguero, J. M., Ding, F., Buldyrev, S. V., Stanley, H. E. & Dokholyan, N. V., Jul 2004, In : Biophysical journal. 87, 1, p. 521-533 13 p.

Research output: Contribution to journalArticle

src Homology Domains
Temperature
Proteins
Molecular Dynamics Simulation
55 Citations (Scopus)

New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate

Dixon, R. D. S., Chen, Y., Ding, F., Khare, S. D., Prutzman, K. C., Schaller, M. D., Campbell, S. L. & Dokholyan, N., Dec 1 2004, In : Structure. 12, 12, p. 2161-2171 11 p.

Research output: Contribution to journalArticle

Focal Adhesion Protein-Tyrosine Kinases
Focal Adhesions
Molecular Dynamics Simulation
Phosphorylation
Paxillin
8 Citations (Scopus)

The evolution dynamics of model proteins

Tiana, G., Dokholyan, N. V., Broglia, R. A. & Shakhnovich, E. I., Aug 1 2004, In : Journal of Chemical Physics. 121, 5, p. 2381-2389 9 p.

Research output: Contribution to journalArticle

proteins
Proteins
set theory
Kinetics
kinetics
105 Citations (Scopus)
Amyotrophic Lateral Sclerosis
Superoxide Dismutase
Metals
Mutation
Superoxide Dismutase-1
9 Citations (Scopus)

What Is the Protein Design Alphabet?

Dokholyan, N. V., Mar 1 2004, In : Proteins: Structure, Function and Genetics. 54, 4, p. 622-628 7 p.

Research output: Contribution to journalArticle

Proteins
Amino Acids
Structural properties
2005
43 Citations (Scopus)

A single disulfide bond differentiates aggregation pathways of ß2-microglobulin

Chen, Y. & Dokholyan, N. V., Nov 25 2005, In : Journal of Molecular Biology. 354, 2, p. 473-482 10 p.

Research output: Contribution to journalArticle

Disulfides
Amyloid
Molecular Dynamics Simulation
Needles
Renal Dialysis
61 Citations (Scopus)

Direct observation of protein folding, aggregation, and a prion-like conformational conversion

Ding, F., LaRocque, J. J. & Dokholyan, N. V., Dec 2 2005, In : Journal of Biological Chemistry. 280, 48, p. 40235-40240 6 p.

Research output: Contribution to journalArticle

Protein folding
Prions
Protein Folding
Agglomeration
Observation
111 Citations (Scopus)

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

Ding, F., Buldyrev, S. V. & Dokholyan, N. V., Jan 2005, In : Biophysical journal. 88, 1, p. 147-155 9 p.

Research output: Contribution to journalArticle

Mechanics
Proteins
Molecular Dynamics Simulation
Amino Acids
64 Citations (Scopus)

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations

Ding, F., Guo, W., Dokholyan, N., Shakhnovich, E. I. & Shea, J. E., Jul 29 2005, In : Journal of Molecular Biology. 350, 5, p. 1035-1050 16 p.

Research output: Contribution to journalArticle

src Homology Domains
Molecular Dynamics Simulation
Proteins
Theoretical Models
Protein Domains