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Research Output 1994 2020

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2009
55 Citations (Scopus)

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

Gherghe, C. M., Leonard, C. W., Ding, F., Dokholyan, N. V. & Weeks, K. M., Feb 25 2009, In : Journal of the American Chemical Society. 131, 7, p. 2541-2546 6 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
RNA
Molecular dynamics
RNA, Transfer, Asp
RNA Folding
84 Citations (Scopus)

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H. M., Jones, D., Brenner, S. E., Burley, S. K., Das, R., Dokholyan, N. V., Dunbrack, R. L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y. J., Humblet, C., Jacobson, M. P., Joachimiak, A., Krystek, S. R., Kortemme, T. & 12 others, Kryshtafovych, A., Montelione, G. T., Moult, J., Murray, D., Sanchez, R., Sosnick, T. R., Standley, D. M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J. D. & Wilson, I. A., Feb 13 2009, In : Structure. 17, 2, p. 151-159 9 p.

Research output: Contribution to journalArticle

Biomedical Research
Education
Proteins
San Francisco
Research
24 Citations (Scopus)

Structural basis for the sequence-dependent effects of platinum - DNA adducts

Ramachandran, S., Temple, B. R., Chaney, S. G. & Dokholyan, N. V., May 29 2009, In : Nucleic acids research. 37, 8, p. 2434-2448 15 p.

Research output: Contribution to journalArticle

oxaliplatin
DNA Adducts
Platinum
Cisplatin
DNA
7 Citations (Scopus)

Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels

Meissner, G., Pasek, D. A., Yamaguchi, N., Ramachandran, S., Dokholyan, N. V. & Tripathy, A., Jan 1 2009, In : Proteins: Structure, Function and Bioinformatics. 74, 1, p. 207-211 5 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Calmodulin
Ion Channels
Thermodynamics
Muscle
2008
185 Citations (Scopus)

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

Ding, F., Tsao, D., Nie, H. & Dokholyan, N., Jul 9 2008, In : Structure. 16, 7, p. 1010-1018 9 p.

Research output: Contribution to journalArticle

Protein Folding
Molecular Dynamics Simulation
Proteins
Hydrogen
Protein Engineering
174 Citations (Scopus)

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E. & Dokholyan, N. V., Jun 1 2008, In : RNA. 14, 6, p. 1164-1173 10 p.

Research output: Contribution to journalArticle

RNA Folding
Molecular Dynamics Simulation
RNA
Base Pairing
RNA, Transfer, Phe
34 Citations (Scopus)

Active nuclear receptors exhibit highly correlated AF-2 domain motions

Teotico, D. G., Frazier, M. L., Ding, F., Dokholyan, N. V., Temple, B. R. S. & Redinbo, M. R., Jul 1 2008, In : PLoS computational biology. 4, 7, e1000111.

Research output: Contribution to journalArticle

Activation Function
Cytoplasmic and Nuclear Receptors
Receptor
ligand
Chemical activation
44 Citations (Scopus)

Computational Studies Reveal Phosphorylation-dependent Changes in the Unstructured R Domain of CFTR

Hegedus, T., Serohijos, A. W. R., Dokholyan, N., He, L. & Riordan, J. R., May 16 2008, In : Journal of Molecular Biology. 378, 5, p. 1052-1063 12 p.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Phosphorylation
Chloride Channels
Cyclic AMP-Dependent Protein Kinases
Cystic Fibrosis
32 Citations (Scopus)

Diminished self-chaperoning activity of the ΔF508 mutant of CFTR results in protein misfolding

Serohijos, A. W. R., Hegedus, T., Riordan, J. R. & Dokholyan, N. V., Feb 1 2008, In : PLoS computational biology. 4, 2

Research output: Contribution to journalArticle

Fibrosis
Cystic Fibrosis Transmembrane Conductance Regulator
cystic fibrosis
ethyl-2-methylthio-4-methyl-5-pyrimidine carboxylate
Conductance
1 Citation (Scopus)

DNA sequence mediates nucleosome structure and stability

Sharma, S. & Dokholyan, N. V., Jan 1 2008, In : Biophysical journal. 94, 1, p. 1-3 3 p.

Research output: Contribution to journalArticle

Nucleosomes
93 Citations (Scopus)
Disulfides
Metals
Ions
Superoxide Dismutase-1
Amyotrophic Lateral Sclerosis
41 Citations (Scopus)

Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers

Hao, J., Serohijos, A. W. R., Newton, G., Tassone, G., Wang, Z., Sgroi, D. C., Dokholyan, N. V. & Basilion, J. P., Aug 1 2008, In : PLoS computational biology. 4, 8, e1000138.

Research output: Contribution to journalArticle

Biomarkers
Tumor Biomarkers
Peptides
peptide
ligand
133 Citations (Scopus)

IFoldRNA: Three-dimensional RNA structure prediction and folding

Sharma, S., Ding, F. & Dokholyan, N. V., Sep 1 2008, In : Bioinformatics. 24, 17, p. 1951-1952 2 p.

Research output: Contribution to journalArticle

Structure Prediction
Folding
RNA
Conformation
Three-dimensional
30 Citations (Scopus)

Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter

Özvegy-Laczka, C., Laczko, R., Hegedus, C., Litman, T., Várady, G., Goda, K., Hegedus, T., Dokholyan, N. V., Sorrentino, B. P., Váradi, A. & Sarkadi, B., Sep 19 2008, In : Journal of Biological Chemistry. 283, 38, p. 26059-26070 12 p.

Research output: Contribution to journalArticle

Dimers
Monoclonal Antibodies
Proteins
Dithiothreitol
Membrane Glycoproteins
94 Citations (Scopus)

MedusaScore: An accurate force field-based scoring function for virtual drug screening

Yin, S., Biedermannova, L., Vondrasek, J. & Dokholyan, N. V., Aug 1 2008, In : Journal of Chemical Information and Modeling. 48, 8, p. 1656-1662 7 p.

Research output: Contribution to journalArticle

Screening
drug
Ligands
Pharmaceutical Preparations
Proteins
91 Citations (Scopus)

Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating

He, L., Aleksandrov, A. A., Serohijos, A. W. R., Hegedus, T., Aleksandrov, L. A., Cui, L., Dokholyan, N. V. & Riordan, J. R., Sep 26 2008, In : Journal of Biological Chemistry. 283, 39, p. 26383-26390 8 p.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Cell Membrane
Membranes
Nucleotides
Adenosine Triphosphate
41 Citations (Scopus)

Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm

Chen, Y. & Dokholyan, N. V., Aug 1 2008, In : Molecular biology and evolution. 25, 8, p. 1530-1533 4 p.

Research output: Contribution to journalArticle

Fungal Proteins
Genetic Selection
natural selection
Diptera
yeast
276 Citations (Scopus)

Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function

Serohijos, A. W. R., Hegedus, T., Aleksandrov, A. A., He, L., Cui, L., Dokholyan, N. V. & Riordan, J. R., Mar 4 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 9, p. 3256-3261 6 p.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Phenylalanine
Cell Membrane
ATP-Binding Cassette Transporters
Endocytosis
2007
50 Citations (Scopus)

Deciphering protein dynamics from NMR data using explicit structure sampling and selection

Chen, Y., Campbell, S. L. & Dokholyan, N. V., Oct 2007, In : Biophysical journal. 93, 7, p. 2300-2306 7 p.

Research output: Contribution to journalArticle

Protein Conformation
Proteins
Information Storage and Retrieval
19 Citations (Scopus)

Fidelity of the protein structure reconstruction from inter-residue proximity constraints

Chen, Y., Ding, F. & Dokholyan, N. V., Jun 28 2007, In : Journal of Physical Chemistry B. 111, 25, p. 7432-7438 7 p.

Research output: Contribution to journalArticle

proximity
proteins
Proteins
Mass spectrometry
Composite materials
14 Citations (Scopus)
Lipids
lipids
Membrane
membranes
Model
113 Citations (Scopus)

Modeling Backbone Flexibility Improves Protein Stability Estimation

Yin, S., Ding, F. & Dokholyan, N. V., Dec 13 2007, In : Structure. 15, 12, p. 1567-1576 10 p.

Research output: Contribution to journalArticle

Protein Stability
Mutation
Proteins
Thermodynamics
Mutagenesis
34 Citations (Scopus)

Molecular Dynamic Simulations of Cisplatin- and Oxaliplatin-d(GG) Intrastand Cross-links Reveal Differences in their Conformational Dynamics

Sharma, S., Gong, P., Temple, B., Bhattacharyya, D., Dokholyan, N. & Chaney, S. G., Nov 9 2007, In : Journal of Molecular Biology. 373, 5, p. 1123-1140 18 p.

Research output: Contribution to journalArticle

oxaliplatin
Molecular Dynamics Simulation
Cisplatin
DNA
Ligands
81 Citations (Scopus)

Multiscale modeling of nucleosome dynamics

Sharma, S., Ding, F. & Dokholyan, N. V., Mar 2007, In : Biophysical journal. 92, 5, p. 1457-1470 14 p.

Research output: Contribution to journalArticle

Nucleosomes
Histones
Chromatin
DNA
Salts
27 Citations (Scopus)

Parallel Folding Pathways in the SH3 Domain Protein

Lam, A. R., Borreguero, J. M., Ding, F., Dokholyan, N., Buldyrev, S. V., Stanley, H. E. & Shakhnovich, E., Nov 9 2007, In : Journal of Molecular Biology. 373, 5, p. 1348-1360 13 p.

Research output: Contribution to journalArticle

src Homology Domains
Proteins
Protein Conformation
Molecular Dynamics Simulation
Amino Acids
9 Citations (Scopus)

Similarity and dissimilarity in correlations of genomic DNA

Podobnik, B., Shao, J., Dokholyan, N., Zlatic, V., Eugene Stanley, H. & Grosse, I., Jan 1 2007, In : Physica A: Statistical Mechanics and its Applications. 373, p. 497-502 6 p.

Research output: Contribution to journalArticle

chromosomes
Dissimilarity
Chromosome
Genomics
deoxyribonucleic acid
37 Citations (Scopus)

The length dependence of the polyQ-mediated protein aggregation

Barton, S., Jacak, R., Khare, S. D., Ding, F. & Dokholyan, N., Aug 31 2007, In : Journal of Biological Chemistry. 282, 35, p. 25487-25492 6 p.

Research output: Contribution to journalArticle

Agglomeration
Proteins
Glutamine
Monomers
Dimers
2006
23 Citations (Scopus)

A structural model reveals energy transduction in dynein

Serohijos, A. W. R., Chen, Y., Ding, F., Elston, T. C. & Dokholyan, N. V., Dec 5 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 49, p. 18540-18545 6 p.

Research output: Contribution to journalArticle

Dyneins
Structural Models
Adenosine Triphosphatases
Electron Microscopy
Kinesin
23 Citations (Scopus)

Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins

Petrotchenko, E. V., Pasek, D., Elms, P., Dokholyan, N. V., Meissner, G. & Borchers, C. H., Dec 1 2006, In : Analytical chemistry. 78, 23, p. 7959-7966 8 p.

Research output: Contribution to journalArticle

Cysteine
Membrane Proteins
Fluorescence
Chemical analysis
Peptides
69 Citations (Scopus)
Mutation
Metals
Protein Stability
Molecular Dynamics Simulation
Point Mutation
146 Citations (Scopus)

Emergence of protein fold families through rational design

Ding, F. & Dokholyan, N. V., Aug 4 2006, In : PLoS computational biology. 2, 7, p. 725-733 9 p.

Research output: Contribution to journalArticle

Fold
fold
Proteins
Protein
protein
34 Citations (Scopus)

FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: A large-scale thermodynamic analysis

Khare, S. D., Caplow, M. & Dokholyan, N. V., Dec 1 2006, In : Amyloid. 13, 4, p. 226-235 10 p.

Research output: Contribution to journalArticle

Thermodynamics
Mutation
Superoxide Dismutase-1
Amyotrophic lateral sclerosis 1
Metals
63 Citations (Scopus)

Fast complementation of split fluorescent protein triggered by DNA hybridization

Demidov, V. V., Dokholyan, N. V., Witte-Hoffmann, C., Chalasani, P., Yiu, H. W., Ding, F., Yu, Y., Cantor, C. R. & Broude, N. E., Feb 14 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 7, p. 2052-2056 5 p.

Research output: Contribution to journalArticle

DNA
Fluorescence
Proteins
Nucleic Acids
Oligonucleotides
32 Citations (Scopus)

iFold: A platform for interactive folding simulations of proteins

Sharma, S., Ding, F., Nie, H., Watson, D., Unnithan, A., Lopp, J., Pozefsky, D. & Dokholyan, N. V., Nov 1 2006, In : Bioinformatics. 22, 21, p. 2693-2694 2 p.

Research output: Contribution to journalArticle

Protein folding
Discrete Dynamics
Protein Folding
Molecular Dynamics Simulation
Folding
24 Citations (Scopus)

Insights into allosteric control of vinculin function from its large scale conformational dynamics

Chen, Y. & Dokholyan, N. V., Sep 29 2006, In : Journal of Biological Chemistry. 281, 39, p. 29148-29154 7 p.

Research output: Contribution to journalArticle

Vinculin
Chemical activation
Talin
Conformations
Binding Sites
63 Citations (Scopus)

Topological determinants of protein domain swapping

Ding, F., Prutzman, K. C., Campbell, S. L. & Dokholyan, N. V., Jan 1 2006, In : Structure. 14, 1, p. 5-14 10 p.

Research output: Contribution to journalArticle

Proteins
Focal Adhesion Protein-Tyrosine Kinases
Focal Adhesions
Molecular Dynamics Simulation
Protein Domains
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
43 Citations (Scopus)

Scaling behavior and structure of denatured proteins

Ding, F., Jha, R. K. & Dokholyan, N., Jul 1 2005, In : Structure. 13, 7, p. 1047-1054 8 p.

Research output: Contribution to journalArticle

Proteins
Molecular Dynamics Simulation
Creatine Kinase
Protein Kinases
Magnetic Resonance Spectroscopy
30 Citations (Scopus)

Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation

Khare, S. D., Wilcox, K. C., Gong, P. & Dokholyan, N. V., Nov 15 2005, In : Proteins: Structure, Function and Genetics. 61, 3, p. 617-632 16 p.

Research output: Contribution to journalArticle

Agglomeration
Proteins
Amyotrophic Lateral Sclerosis
Molecular Dynamics Simulation
Point Mutation
56 Citations (Scopus)

Simple but predictive protein models

Ding, F. & Dokholyan, N., Jan 1 2005, In : Trends in Biotechnology. 23, 9, p. 450-455 6 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Proteins
Molecular dynamics
Computer simulation
Biophysics
15 Citations (Scopus)

The architecture of the protein domain universe

Dokholyan, N. V., Mar 14 2005, In : Gene. 347, 2 SPEC. ISS., p. 199-206 8 p.

Research output: Contribution to journalArticle

Proteins
Statistical Models
Mechanics
Protein Domains
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
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
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
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