If you made any changes in Pure, your changes will be visible here soon.

Research Output 1994 2020

Filter
Article
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

A central core disease mutation in the Ca2+-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation

Chirasani, V. R., Xu, L., Addis, H. G., Pasek, D. A., Dokholyan, N. V., Meissner, G. & Yamaguchi, N., Aug 2019, In : American Journal of Physiology - Cell Physiology. 317, 2, p. C358-C365

Research output: Contribution to journalArticle

Central Core Myopathy
Ryanodine Receptor Calcium Release Channel
Skeletal Muscle
Binding Sites
Mutation
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
16 Citations (Scopus)

A didactic model of macromolecular crowding effects on protein folding

Tsao, D., Minton, A. P. & Dokholyan, N. V., Oct 15 2010, In : PloS one. 5, 8, e11936.

Research output: Contribution to journalArticle

Protein folding
protein folding
Protein Folding
toys
Play and Playthings
1 Citation (Scopus)

A folding pathway-dependent score to recognize membrane proteins

Hadi-Alijanvand, H., Rouhani, M., Proctor, E. A., Dokholyan, N. V. & Moosavi-Movahedi, A. A., Mar 10 2011, In : PloS one. 6, 3, e16778.

Research output: Contribution to journalArticle

membrane proteins
Membrane Proteins
Membranes
proteins
Proteins
1 Citation (Scopus)

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V. & Moosavi-Movahedi, A. A., May 1 2016, In : Proteins: Structure, Function and Bioinformatics. 84, 5, p. 611-623 13 p.

Research output: Contribution to journalArticle

Prolyl Hydroxylases
Agglomeration
Protein Unfolding
Proteins
Molecular Dynamics Simulation
56 Citations (Scopus)

Allosteric modulation balances thermodynamic stability and restores function of Δf508 CFTR

Aleksandrov, A. A., Kota, P., Cui, L., Jensen, T., Alekseev, A. E., Reyes, S., He, L., Gentzsch, M., Aleksandrov, L. A., Dokholyan, N. V. & Riordan, J. R., May 25 2012, In : Journal of Molecular Biology. 419, 1-2, p. 41-60 20 p.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Thermodynamics
Proline
Genetic Suppression
Transition Temperature
12 Citations (Scopus)

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

Chandrasekaran, S. N., Das, J., Dokholyan, N. V. & Carter, C. W., Jan 1 2016, In : Structural Dynamics. 3, 1, 012101.

Research output: Contribution to journalArticle

Proteins
Structural properties
Crystal structure
Trajectories
proteins
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
11 Citations (Scopus)

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation

Fay, J. M., Zhu, C., Proctor, E. A., Tao, Y., Cui, W., Ke, H. & Dokholyan, N. V., Nov 1 2016, In : Structure. 24, 11, p. 1898-1906 9 p.

Research output: Contribution to journalArticle

Amyotrophic Lateral Sclerosis
Cell Survival
Mutation
Poisons
Motor Neurons
9 Citations (Scopus)

A physical model reveals the mechanochemistry responsible for Dynein's processive motion

Tsygankov, D., Serohijos, A. W. R., Dokholyan, N. & Elston, T. C., Jul 6 2011, In : Biophysical journal. 101, 1, p. 144-150 7 p.

Research output: Contribution to journalArticle

Dyneins
Stroke
Head
Microtubules
Binding Sites
11 Citations (Scopus)

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

Williams, B., Convertino, M., Das, J. & Dokholyan, N. V., Jan 1 2015, In : PLoS computational biology. 11, 10, e1004359.

Research output: Contribution to journalArticle

Apolipoprotein E4
Alzheimer's Disease
molecular dynamics
Molecular Dynamics Simulation
Alzheimer disease
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
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
6 Citations (Scopus)

A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization

Thompson, P. M., Ramachandran, S., Case, L. B., Tolbert, C. E., Tandon, A., Pershad, M., Dokholyan, N. V., Waterman, C. M. & Campbell, S. L., Feb 7 2017, In : Structure. 25, 2, p. 264-275 12 p.

Research output: Contribution to journalArticle

Vinculin
Structural Models
Focal Adhesions
Membranes
Lipid Bilayers
24 Citations (Scopus)

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)

Ramachandran, S., Serohijos, A. W. R., Xu, L., Meissner, G. & Dokholyan, N. V., Apr 1 2009, In : PLoS computational biology. 5, 4

Research output: Contribution to journalArticle

ryanodine receptors
Ryanodine Receptor Calcium Release Channel
Skeletal muscle
Structural Models
Structural Model
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
36 Citations (Scopus)

ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions

Gyimesi, G., Ramachandran, S., Kota, P., Dokholyan, N. V., Sarkadi, B. & Hegedus, T., Dec 1 2011, In : Biochimica et Biophysica Acta - Biomembranes. 1808, 12, p. 2954-2964 11 p.

Research output: Contribution to journalArticle

ATP-Binding Cassette Transporters
Hydrolysis
Nucleotides
Adenosine Triphosphate
Conformations
135 Citations (Scopus)

Automated minimization of steric clashes in protein structures

Ramachandran, S., Kota, P., Ding, F. & Dokholyan, N. V., Jan 1 2011, In : Proteins: Structure, Function and Bioinformatics. 79, 1, p. 261-270 10 p.

Research output: Contribution to journalArticle

Proteins
Benchmarking
Atoms
Molecular modeling
Artifacts
47 Citations (Scopus)

BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics

Petrotchenko, E. V., Xiao, K., Cable, J., Chen, Y., Dokholyan, N. V. & Borchers, C. H., Feb 1 2009, In : Molecular and Cellular Proteomics. 8, 2, p. 273-286 14 p.

Research output: Contribution to journalArticle

Proteomics
Peptides
Proteins
Mass spectrometry
Gels
2 Citations (Scopus)

Ca 2 -mediated activation of the skeletal-muscle ryanodine receptor ion channel

Xu, L., Chirasani, V. R., Carter, J. S., Pasek, D. A., Dokholyan, N. V., Yamaguchi, N. & Meissner, G., Jan 1 2018, In : Journal of Biological Chemistry. 293, 50, p. 19501-19509 9 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Ion Channels
Muscle
Skeletal Muscle
Chemical activation
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
1 Citation (Scopus)

Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies

Sarker, M., Lee, H. T., Mei, L., Krokhotin, A., de los Reyes, S. E., Yen, L., Costantini, L. M., Griffith, J., Dokholyan, N., Alushin, G. M. & Campbell, S. L., Apr 5 2019, In : Journal of Molecular Biology. 431, 8, p. 1604-1618 15 p.

Research output: Contribution to journalArticle

Vinculin
Cardiomyopathies
Actins
Mutation
Dimerization
9 Citations (Scopus)

Channel gating dependence on pore lining helix glycine residues in skeletal muscle ryanodine receptor

Mei, Y., Xu, L., Mowrey, D. D., Giraldez, R. M., Wang, Y., Pasek, D. A., Dokholyan, N. V. & Meissner, G., Jul 10 2015, In : Journal of Biological Chemistry. 290, 28, p. 17535-17545 11 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Linings
Glycine
Muscle
Skeletal Muscle
26 Citations (Scopus)
Molecular mechanics
mechanic
Screening
knowledge
Ligands
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
19 Citations (Scopus)

Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets

Hsieh, J. H., Yin, S., Liu, S., Sedykh, A., Dokholyan, N. V. & Tropsha, A., Sep 26 2011, In : Journal of Chemical Information and Modeling. 51, 9, p. 2027-2035 9 p.

Research output: Contribution to journalArticle

Ligands
Proteins
Testing
interaction
performance
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
232 Citations (Scopus)

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

Michino, M., Abola, E., Brooks, C. L., Scott Dixon, J., Moult, J., Stevens, R. C., Olson, A., Jurkowski, W., Elofsson, A., Filipek, S., Pogozheva, I., Lomize, A., Maigret, B., Horst, J., Roy, A., Bernard, B., Iyer, S., Zhang, Y., Samudrala, R., Sezerman, O. U. & 43 others, Nikiforovich, G. V., Taylor, C. M., Costanzi, S., Vorobjev, Y., Bakulina, N., Solovyev, V., Kanou, K., Takaya, D., Terashi, G., Takeda-Shitaka, M., Umeyama, H., Goddard, W. A., Li, Y., Kim, S. K., Trzaskowski, B., Abrol, R., Griffith, A., Katritch, V., Rueda, M., Abagyan, R., Davis, I., Barth, P., Baker, D., Feig, M., Brylinski, M., Zhou, H., Lee, S. Y., Skolnick, J., Ostopovici-Halip, L., Bologa, C., Lam, P., Abagyan, R., Dawson, E. S., Kaufmann, K., Woetzel, N., Meiler, J., Ding, F., Serohijos, A., Yin, S., Dokholyan, N., Rodriguez, D., Gutiérrez-de-Teràn, H. & Xhaard, H., Jan 1 2009, In : Nature Reviews Drug Discovery. 8, 6, p. 455-463 9 p.

Research output: Contribution to journalArticle

G-Protein-Coupled Receptors
Ligands
Drug Design
Structural Models
Protein Transport
10 Citations (Scopus)

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

Woods, C. T., Lackey, L., Williams, B., Dokholyan, N. V., Gotz, D. & Laederach, A., Jul 25 2017, In : Biophysical journal. 113, 2, p. 290-301 12 p.

Research output: Contribution to journalArticle

RNA
Acylation
Hydroxyl Radical
Adenine
Riboswitch
55 Citations (Scopus)

Computational Design of a PAK1 Binding Protein

Jha, R. K., Leaver-Fay, A., Yin, S., Wu, Y., Butterfoss, G. L., Szyperski, T., Dokholyan, N. & Kuhlman, B., Jul 1 2010, In : Journal of Molecular Biology. 400, 2, p. 257-270 14 p.

Research output: Contribution to journalArticle

p21-Activated Kinases
Spiders
Carrier Proteins
Proteins
Molecular Probes
8 Citations (Scopus)

Computational design of chemogenetic and optogenetic split proteins

Dagliyan, O., Krokhotin, A., Ozkan-Dagliyan, I., Deiters, A., Der, C. J., Hahn, K. M. & Dokholyan, N. V., Dec 1 2018, In : Nature communications. 9, 1, 4042.

Research output: Contribution to journalArticle

Optogenetics
proteins
Proteins
assembly
Biological Phenomena

Computationally Guided Design of Single-Chain Variable Fragment Improves Specificity of Chimeric Antigen Receptors

Krokhotin, A., Du, H., Hirabayashi, K., Popov, K., Kurokawa, T., Wan, X., Ferrone, S., Dotti, G. & Dokholyan, N. V., Dec 20 2019, In : Molecular Therapy - Oncolytics. 15, p. 30-37 8 p.

Research output: Contribution to journalArticle

Open Access
Single-Chain Antibodies
Antigen Receptors
T-Cell Antigen Receptor
Peptides
Antibody Specificity
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
13 Citations (Scopus)

COMT gene locus: New functional variants

Meloto, C. B., Segall, S. K., Smith, S., Parisien, M., Shabalina, S. A., Rizzatti-Barbosa, C. M., Gauthier, J., Tsao, D., Convertino, M., Piltonen, M. H., Slade, G. D., Fillingim, R. B., Greenspan, J. D., Ohrbach, R., Knott, C., Maixner, W., Zaykin, D., Dokholyan, N. V., Reenila, I., Mannisto, P. T. & 1 others, Diatchenko, L., Oct 2015, In : Pain. 156, 10, p. 2072-2083 12 p.

Research output: Contribution to journalArticle

Catechol O-Methyltransferase
Genes
Pain
Protein Isoforms
Adrenergic Agents
4 Citations (Scopus)

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

Brodie, N. I., Popov, K. I., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Mar 2019, In : PLoS computational biology. 15, 3, e1006859.

Research output: Contribution to journalArticle

Open Access
Synucleins
Discrete Dynamics
molecular dynamics
protein structure
Molecular Dynamics Simulation
80 Citations (Scopus)

Correctors of δF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

He, L., Kota, P., Aleksandrov, A. A., Cui, L., Jensen, T., Dokholyan, N. V. & Riordan, J. R., Feb 2013, In : FASEB Journal. 27, 2, p. 536-545 10 p.

Research output: Contribution to journalArticle

Mutant Proteins
Investigational Drugs
Proteolysis
Thermodynamics
Cystic Fibrosis
23 Citations (Scopus)

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive

Nedd, S., Redler, R. L., Proctor, E. A., Dokholyan, N. V. & Alexandrova, A. N., Dec 12 2014, In : Journal of Molecular Biology. 426, 24, p. 4112-4124 13 p.

Research output: Contribution to journalArticle

Protein Unfolding
Amyotrophic Lateral Sclerosis
Molecular Dynamics Simulation
Mechanics
Superoxides
175 Citations (Scopus)

Cystic fibrosis: Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

Cholon, D. M., Quinney, N. L., Fulcher, M. L., Esther, C. R., Das, J., Dokholyan, N., Randell, S. H., Boucher, R. C. & Gentzsch, M., Jul 23 2014, In : Science Translational Medicine. 6, 246, 246ra96.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Cystic Fibrosis
Pharmacology
Mutation
Therapeutics
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
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
12 Citations (Scopus)

Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers

Martin, L. J., Piltonen, M. H., Gauthier, J., Convertino, M., Acland, E. L., Dokholyan, N., Mogil, J. S., Diatchenko, L. & Maixner, W., Jan 1 2015, In : Journal of Pain. 16, 12, p. 1321-1333 13 p.

Research output: Contribution to journalArticle

Bupranolol
Propranolol
Adrenergic Receptors
Adrenergic Agonists
Pain
9 Citations (Scopus)

Differential regulation of 6- and 7-Transmembrane helix variants of μ-opioid receptor in response to morphine stimulation

Convertino, M., Samoshkin, A., Viet, C. T., Gauthier, J., Fraine, S. P. L., Sharif-Naeini, R., Schmidt, B. L., Maixner, W., Diatchenko, L. & Dokholyan, N. V., Nov 10 2015, In : PloS one. 10, 11, e0142826.

Research output: Contribution to journalArticle

morphine
narcotics
Opioid Receptors
Morphine
Opioid Analgesics
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
11 Citations (Scopus)

Direct identification of base-paired RNA nucleotides by correlated chemical probing

Krokhotin, A., Mustoe, A. M., Weeks, K. M. & Dokholyan, N. V., Jan 2017, In : RNA. 23, 1, p. 6-13 8 p.

Research output: Contribution to journalArticle

Nucleotides
RNA
Base Pairing
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
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
94 Citations (Scopus)

Discrete molecular dynamics: An efficient and versatile simulation method for fine protein characterization

Shirvanyants, D., Ding, F., Tsao, D., Ramachandran, S. & Dokholyan, N. V., Jul 26 2012, In : Journal of Physical Chemistry B. 116, 29, p. 8375-8382 8 p.

Research output: Contribution to journalArticle

folding
Molecular dynamics
molecular dynamics
proteins
Proteins