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2017
2 Citations

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: Research - peer-reviewArticle

Vinculin
Structural Models
Membranes
Focal Adhesions
Lipid Bilayers
1 Citations

Computational protein design through grafting and stabilization

Zhu, C., Mowrey, D. D. & Dokholyan, N. V. 2017 Methods in Molecular Biology. Humana Press Inc., Vol. 1529, p. 227-241 15 p. (Methods in Molecular Biology; vol. 1529)

Research output: ResearchChapter

Proteins
Mutation
Protein Stability
Software
Databases
2 Citations

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

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

Research output: Research - peer-reviewArticle

Nucleotides
RNA
Base Pairing
dimethyl sulfate
2016

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: Research - peer-reviewArticle

Prolyl Hydroxylases
Hypoxia
Agglomeration
Proteins
Protein Domains
8 Citations

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: Research - peer-reviewArticle

Proteins
Structural properties
Crystal structure
Trajectories
proteins
2 Citations

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: Research - peer-reviewArticle

Amyotrophic Lateral Sclerosis
Cell Survival
Mutation
Poisons
Motor Neurons
9 Citations

Applications of Discrete Molecular Dynamics in biology and medicine

Proctor, E. A. & Dokholyan, N. V. Apr 1 2016 In : Current Opinion in Structural Biology. 37, p. 9-13 5 p.

Research output: Research - peer-reviewArticle

Molecular Dynamics Simulation
Medicine
Proteins
Microcomputers
Proteostasis Deficiencies
17 Citations

Controlling Allosteric Networks in Proteins

Dokholyan, N. V. Jun 8 2016 In : Chemical Reviews. 116, 11, p. 6463-6487 25 p.

Research output: Research - peer-reviewReview article

Proteins
Ligands
Cystic Fibrosis Transmembrane Conductance Regulator
Biological systems
Binding Sites
4 Citations
Factor Xa
Classifiers
Ligands
activity structure
ranking
9 Citations

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications

Allen, S. E., Dokholyan, N. V. & Bowers, A. A. Jan 15 2016 In : ACS Chemical Biology. 11, 1, p. 10-24 15 p.

Research output: Research - peer-reviewReview article

Biological Products
Scaffolds
Proteins
Point contacts
Pharmaceutical Chemistry
11 Citations

Engineering extrinsic disorder to control protein activity in living cells

Dagliyan, O., Tarnawski, M., Chu, P. H., Shirvanyants, D., Schlichting, I., Dokholyan, N. V. & Hahn, K. M. Dec 16 2016 In : Science. 354, 6318, p. 1441-1444 4 p.

Research output: Research - peer-reviewArticle

Proteins
Molecular Motor Proteins
Optogenetics
Guanosine
Guanine
1 Citations

Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit coupling

Shobair, M., Dagliyan, O., Kota, P., Dang, Y. L., He, H., Stutts, M. J. & Dokholyan, N. V. Feb 19 2016 In : Journal of Biological Chemistry. 291, 8, p. 3682-3692 11 p.

Research output: Research - peer-reviewArticle

Epithelial Sodium Channels
Chemical activation
Mutation
Molecular dynamics
Sodium
12 Citations

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

Proctor, E. A., Fee, L., Tao, Y., Redler, R. L., Fay, J. M., Zhang, Y., Lv, Z., Mercer, I. P., Deshmukh, M., Lyubchenko, Y. L. & Dokholyan, N. V. Jan 19 2016 In : Proceedings of the National Academy of Sciences of the United States of America. 113, 3, p. 614-619 6 p.

Research output: Research - peer-reviewArticle

Poisons
Amyotrophic Lateral Sclerosis
Motor Neurons
Mutation
Therapeutics
17 Citations

Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases

Convertino, M., Das, J. & Dokholyan, N. V. Jun 17 2016 In : ACS Chemical Biology. 11, 6, p. 1471-1489 19 p.

Research output: Research - peer-reviewReview article

Pharmacology
Proteins
Therapeutics
Poisons
Protein Folding
4 Citations

Protein Destabilization as a Common Factor in Diverse Inherited Disorders

Redler, R. L., Das, J., Diaz, J. R. & Dokholyan, N. V. Jan 1 2016 In : Journal of Molecular Evolution. 82, 1, p. 11-16 6 p.

Research output: Research - peer-reviewLetter

genetic disorders
proteins
protein
Proteins
mutation
5 Citations

Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770

Gentzsch, M., Ren, H. Y., Houck, S. A., Quinney, N. L., Cholon, D. M., Sopha, P., Chaudhry, I. G., Das, J., Dokholyan, N. V., Randell, S. H. & Cyr, D. M. Jan 1 2016 In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 311, 3, p. L550-L559

Research output: Research - peer-reviewArticle

Therapeutics
lumacaftor
ivacaftor
Cystic Fibrosis
Mutation
2015
9 Citations

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

Williams, B., Convertino, M., Das, J. & Dokholyan, N. V. 2015 In : PLoS Computational Biology. 11, 10, e1004359

Research output: Research - peer-reviewArticle

protein isoforms
apolipoprotein E
molecular dynamics
homeostasis
risk factors
6 Citations

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: Research - peer-reviewArticle

Ryanodine Receptor Calcium Release Channel
Glycine
Skeletal Muscle
Linings
Muscle
5 Citations

Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models

Krokhotin, A. & Dokholyan, N. V. Jan 1 2015 In : Methods in Enzymology. 553, p. 65-89 25 p.

Research output: Research - peer-reviewReview article

Computational methods
RNA
Atoms
Nucleotides
Computer simulation
5 Citations

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 1 2015 In : Pain. 156, 10, p. 2072-2083 12 p.

Research output: Research - peer-reviewArticle

Catechol O-Methyltransferase
Genes
Pain
Protein Isoforms
Adrenergic Agents
3 Citations

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. V., Mogil, J. S., Diatchenko, L. & Maixner, W. Jan 1 2015 In : Journal of Pain. 16, 12, p. 1321-1333 13 p.

Research output: Research - peer-reviewArticle

Bupranolol
Propranolol
Adrenergic beta-Agonists
Receptors, Adrenergic, beta
Adrenergic Receptors
6 Citations

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: Research - peer-reviewArticle

mu Opioid Receptor
Morphine
Opioid Analgesics
morphine
narcotics
11 Citations

iFoldRNA v2: Folding RNA with constraints

Krokhotin, A., Houlihan, K. & Dokholyan, N. V. Feb 6 2015 In : Bioinformatics. 31, 17, p. 2891-2893 3 p.

Research output: Research - peer-reviewArticle

Folding
RNA Folding
RNA
Server
Prediction
8 Citations

Light-cleavable rapamycin dimer as an optical trigger for protein dimerization

Brown, K. A., Zou, Y., Shirvanyants, D., Zhang, J., Samanta, S., Mantravadi, P. K., Dokholyan, N. V. & Deiters, A. Apr 4 2015 In : Chemical Communications. 51, 26, p. 5702-5705 4 p.

Research output: Research - peer-reviewArticle

Tacrolimus Binding Protein 1A
Dimerization
Sirolimus
Dimers
Proteins
6 Citations

Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX

Wang, L., Xie, L., Ramachandran, S., Lee, Y. Y., Yan, Z., Zhou, L., Krajewski, K., Liu, F., Zhu, C., Chen, D. J., Strahl, B. D., Jin, J., Dokholyan, N. V. & Chen, X. Jul 24 2015 In : Chemistry and Biology. 22, 7, p. 849-861 13 p., 3066

Research output: Research - peer-reviewArticle

Lysine
DNA Damage
DNA
Radiation
Neoplasms
13 Citations
Cystic Fibrosis Transmembrane Conductance Regulator
Proteins
Ion Channels
Nucleotides
8 Citations

Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling

Samoshkin, A., Convertino, M., Viet, C. T., Wieskopf, J. S., Kambur, O., Marcovitz, J., Patel, P., Stone, L. S., Kalso, E., Mogil, J. S., Schmidt, B. L., Maixner, W., Dokholyan, N. V. & Diatchenko, L. Dec 11 2015 In : Scientific Reports. 5, 18198

Research output: Research - peer-reviewArticle

mu Opioid Receptor
Opioid Analgesics
Ligands
Calcium
Adrenergic beta-2 Receptors
8 Citations

μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids

Convertino, M., Samoshkin, A., Gauthier, J., Gold, M. S., Maixner, W., Dokholyan, N. V. & Diatchenko, L. Oct 1 2015 In : Progress in Neuro-Psychopharmacology and Biological Psychiatry. 62, p. 61-67 7 p.

Research output: Research - peer-reviewArticle

mu Opioid Receptor
Opioid Analgesics
Protein Isoforms
Therapeutics
Hyperalgesia
2014
2 Citations

Computational approaches to understanding protein aggregation in neurodegeneration

Redler, R. L., Shirvanyants, D., Dagliyan, O., Ding, F., Kim, D. N., Kota, P., Proctor, E. A., Ramachandran, S., Tandon, A. & Dokholyan, N. V. 2014 In : Japanese Journal of Clinical Oncology. 6, 2, p. 104-115 12 p., mju007

Research output: Research - peer-reviewReview article

Proteins
Poisons
Amyotrophic Lateral Sclerosis
Information Systems
Neurodegenerative Diseases
7 Citations

Computational approaches to understanding protein aggregation in neurodegeneration

Redler, R. L., Shirvanyants, D., Dagliyan, O., Ding, F., Kim, D. N., Kota, P., Proctor, E. A., Ramachandran, S., Tandon, A. & Dokholyan, N. V. 2014 In : Journal of Molecular Cell Biology. 6, 2, p. 104-115 12 p.

Research output: Research - peer-reviewReview article

Proteins
Poisons
Amyotrophic Lateral Sclerosis
Information Systems
Neurodegenerative Diseases
Mutant Proteins
11 Citations

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: Research - peer-reviewArticle

Superoxide Dismutase-1
Protein Unfolding
Amyotrophic Lateral Sclerosis
Molecular Dynamics Simulation
Mechanics
111 Citations

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. V., Randell, S. H., Boucher, R. C. & Gentzsch, M. Jul 23 2014 In : Science Translational Medicine. 6, 246, 246ra96

Research output: Research - peer-reviewArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Cystic Fibrosis
Pharmacology
ivacaftor
Therapeutics
10 Citations

Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins

Szöllosi, D., Horváth, T., Han, K. H., Dokholyan, N. V., Tompa, P., Kalmár, L. & Hegedus, T. Apr 24 2014 In : PLoS One. 9, 4, e95795

Research output: Research - peer-reviewArticle

Molecular dynamics
Proteins
Molecular Dynamics Simulation
molecular dynamics
proteins
21 Citations

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties

Thompson, P. M., Tolbert, C. E., Shen, K., Kota, P., Palmer, S. M., Plevock, K. M., Orlova, A., Galkin, V. E., Burridge, K., Egelman, E. H., Dokholyan, N. V., Superfine, R. & Campbell, S. L. May 6 2014 In : Structure. 22, 5, p. 697-706 10 p.

Research output: Research - peer-reviewArticle

Vinculin
Focal Adhesions
Cell Adhesion
Actins
Adherens Junctions
8 Citations

Intrinsic disorder mediates cooperative signal transduction in STIM1

Furukawa, Y., Teraguchi, S., Ikegami, T., Dagliyan, O., Jin, L., Hall, D., Dokholyan, N. V., Namba, K., Akira, S., Kurosaki, T., Baba, Y. & Standley, D. M. May 15 2014 In : Journal of Molecular Biology. 426, 10, p. 2082-2097 16 p.

Research output: Research - peer-reviewArticle

Signal Transduction
Sterile Alpha Motif
Dimerization
Proteins
Structural Models
11 Citations

Non-native soluble oligomers of Cu/Zn superoxide dismutase (SOD1) contain a conformational epitope linked to cytotoxicity in amyotrophic lateral sclerosis (ALS)

Redler, R. L., Fee, L., Fay, J. M., Caplow, M. & Dokholyan, N. V. Apr 15 2014 In : Biochemistry. 53, 14, p. 2423-2432 10 p.

Research output: Research - peer-reviewArticle

Cytotoxicity
Oligomers
Epitopes
Superoxide Dismutase
Amyotrophic Lateral Sclerosis
5 Citations

Pore dynamics and conductance of RyR1 transmembrane domain

Shirvanyants, D., Ramachandran, S., Mei, Y., Xu, L., Meissner, G. & Dokholyan, N. V. Jun 3 2014 In : Biophysical Journal. 106, 11, p. 2375-2384 10 p.

Research output: Research - peer-reviewArticle

Ryanodine Receptor Calcium Release Channel
Central Core Myopathy
Mutation
Cryoelectron Microscopy
Malignant Hyperthermia
6 Citations

RNA tertiary structure analysis by 2?-Hydroxyl molecular interference

Homan, P. J., Tandon, A., Rice, G. M., Ding, F., Dokholyan, N. V. & Weeks, K. M. Nov 4 2014 In : Biochemistry. 53, 43, p. 6825-6833 9 p.

Research output: Research - peer-reviewArticle

Hydroxyl Radical
RNA
octogen
Guide RNA
Introns
29 Citations

Single-molecule correlated chemical probing of RNA

Homan, P. J., Favorov, O. V., Lavender, C. A., Kursun, O., Ge, X., Busan, S., Dokholyan, N. V. & Weeks, K. M. Sep 23 2014 In : Proceedings of the National Academy of Sciences of the United States of America. 111, 38, p. 13858-13863 6 p.

Research output: Research - peer-reviewArticle

RNA
RNA Folding
High-Throughput Nucleotide Sequencing
Nucleic Acids
Nucleotides
9 Citations

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

Kimura, S., Caldarini, M., Broglia, R. A., Dokholyan, N. V. & Tiana, G. 2014 In : Proteins: Structure, Function and Bioinformatics. 82, 4, p. 633-639 7 p.

Research output: Research - peer-reviewArticle

Conformations
Molecular dynamics
Monomers
Proteins
Human immunodeficiency virus 1 p16 protease
4 Citations

The N-terminal domain allosterically regulates cleavage and activation of the epthelial sodium channel

Kota, P., Buchner, G., Chakraborty, H., Dang, Y. L., He, H., Garcia, G. J. M., Kubelka, J., Gentzsch, M., Stutts, M. J. & Dokholyan, N. V. Aug 15 2014 In : Journal of Biological Chemistry. 289, 33, p. 23029-23042 14 p.

Research output: Research - peer-reviewArticle

Epithelial Sodium Channels
Sodium Channels
Chemical activation
Peptide Hydrolases
Phosphatidylinositols
6 Citations

Traffic within the cytochrome b6f lipoprotein complex: Gating of the quinone portal

Hasan, S. S., Proctor, E. A., Yamashita, E., Dokholyan, N. V. & Cramer, W. A. Oct 7 2014 In : Biophysical Journal. 107, 7, p. 1620-1628 9 p.

Research output: Research - peer-reviewArticle

Hydroquinones
Cytochromes b
Lipoproteins
benzoquinone
Superoxides
2013

Correction: Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: Computational approaches (PLoS ONE)

Hadi-Alijanvand, H., Proctor, E. A., Goliaei, B., Dokholyan, N. V. & Moosavi-Movahedi, A. A. Apr 22 2013 In : PLoS One. 8, 4

Research output: Research - peer-reviewComment/debate

active sites
heat
Catalytic Domain
Hot Temperature
65 Citations

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: Research - peer-reviewArticle

Mutant Proteins
lumacaftor
Investigational Drugs
Proteolysis
Quality control
19 Citations

Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability

Chong, P. A., Kota, P., Dokholyan, N. V. & Forman-Kay, J. D. Mar 2013 In : Cold Spring Harbor perspectives in medicine. 3, 3, a009522

Research output: Research - peer-reviewArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Nucleotides
Excited states
Sampling
Phosphorylation
4 Citations

Highly covarying residues have a functional role in antibody constant domains

Proctor, E. A., Kota, P., Demarest, S. J., Caravella, J. A. & Dokholyan, N. V. May 2013 In : Proteins: Structure, Function and Bioinformatics. 81, 5, p. 884-895 12 p.

Research output: Research - peer-reviewArticle

Antibodies
Proteins
Mutation
Antibody Specificity
Immunoglobulin Isotypes
10 Citations

Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): Structural and thermodynamic basis of CIB1 promiscuity

Freeman, T. C., Black, J. L., Bray, H. G., Dagliyan, O., Wu, Y. I., Tripathy, A., Dokholyan, N. V., Leisner, T. M. & Parise, L. V. Oct 8 2013 In : Biochemistry. 52, 40, p. 7082-7090 9 p.

Research output: Research - peer-reviewArticle

Integrins
Carrier Proteins
Thermodynamics
Calcium
Calcium-Binding Proteins
19 Citations
Benchmarking
Ligands
flexibility
drug
ranking
23 Citations

Knowledge-based design of a biosensor to quantify localized ERK activation in living cells

Kummer, L., Hsu, C. W., Dagliyan, O., MacNevin, C., Kaufholz, M., Zimmermann, B., Dokholyan, N. V., Hahn, K. M. & Plückthun, A. Jun 20 2013 In : Chemistry and Biology. 20, 6, p. 847-856 10 p.

Research output: Research - peer-reviewArticle

Biosensors
Chemical activation
Cells
Biosensing Techniques
Proteins