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Research Output 1994 2020

2020

Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations

Makepeace, K. A. T., Brodie, N. I., Popov, K. I., Gudavicius, G., Nelson, C. J., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Jan 16 2020, In : Journal of Proteomics. 211, 103544.

Research output: Contribution to journalArticle

Open Access
Molecular Dynamics Simulation
Proteomics
Molecular dynamics
Ligands
Computer simulation
2019

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
12 Citations (Scopus)

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J. P., Bolhuis, P. G., Vreede, J., Faccioli, P. & 19 others, Orioli, S., Ravasio, R., Yan, L., Brito, C., Wyart, M., Gkeka, P., Rivalta, I., Palermo, G., McCammon, J. A., Panecka-Hofman, J., Wade, R. C., Di Pizio, A., Niv, M. Y., Nussinov, R., Tsai, C. J., Jang, H., Padhorny, D., Kozakov, D. & McLeish, T., Apr 2 2019, In : Structure. 27, 4, p. 566-578 13 p.

Research output: Contribution to journalReview article

Allosteric Regulation
Biological Phenomena
Education
Drug Design
Signal Transduction
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

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., 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
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

Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences

Krokhotin, A., Sarker, M., Sevilla, E. A., Costantini, L. M., Griffith, J. D., Campbell, S. L. & Dokholyan, N. V., Oct 1 2019, In : Structure. 27, 10, p. 1527-1536.e3

Research output: Contribution to journalArticle

Vinculin
Actins
Protein Isoforms
Actin Cytoskeleton
Point Mutation
1 Citation (Scopus)

Engineering proteins for allosteric control by light or ligands

Dagliyan, O., Dokholyan, N. & Hahn, K. M., Jun 1 2019, In : Nature Protocols. 14, 6, p. 1863-1883 21 p.

Research output: Contribution to journalArticle

Protein Engineering
Ligands
Light
Guanine
Sirolimus
1 Citation (Scopus)

Insight into the Structure of the “Unstructured” Tau Protein

Popov, K. I., Makepeace, K. A. T., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Nov 5 2019, In : Structure. 27, 11, p. 1710-1715.e4

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
tau Proteins
Molecular Dynamics Simulation
Proteomics
Proteins

Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase

Sapienza, P. J., Popov, K. I., Mowrey, D. D., Falk, B. T., Dokholyan, N. & Lee, A. L., Jul 30 2019, In : Biochemistry. 58, 30, p. 3302-3313 12 p.

Research output: Contribution to journalArticle

Thymidylate Synthase
Dimers
Catalytic Domain
Nuclear magnetic resonance
Magnetic Resonance Spectroscopy

Limits in accuracy and a strategy of RNA structure prediction using experimental information

Wang, J., Williams, B., Chirasani, V. R., Krokhotin, A., Das, R. & Dokholyan, N. V., Jan 1 2019, In : Nucleic acids research. 47, 11, p. 5563-5572 10 p.

Research output: Contribution to journalArticle

Open Access
RNA
Structural Models
Computational Biology
1 Citation (Scopus)

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking with Constraints

Wang, J. & Dokholyan, N., Jun 24 2019, In : Journal of Chemical Information and Modeling. 59, 6, p. 2509-2515 7 p.

Research output: Contribution to journalArticle

Ligands
drug
Proteins
efficiency
energy
2 Citations (Scopus)

MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression

Jiang, Y., Zhang, Y., Leung, J. Y., Fan, C., Popov, K. I., Su, S., Qian, J., Wang, X., Holtzhausen, A., Ubil, E., Xiang, Y., Davis, I., Dokholyan, N., Wu, G., Perou, C. M., Kim, W. Y., Earp, H. S. & Liu, P., Dec 1 2019, In : Nature communications. 10, 1, 1515.

Research output: Contribution to journalArticle

Open Access
phosphorylation
Phosphorylation
Chemical activation
retarding
activation
2 Citations (Scopus)

Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins

Bonfanti, S., Lionetti, M. C., Fumagalli, M. R., Chirasani, V. R., Tiana, G., Dokholyan, N. V., Zapperi, S. & La Porta, C. A. M., Dec 1 2019, In : Scientific reports. 9, 1, 7615.

Research output: Contribution to journalArticle

Open Access
Huntington Disease
Molecular Conformation
Fluorescence Resonance Energy Transfer
Prions
Optical Imaging
1 Citation (Scopus)

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

Zhu, C., Dukhovlinova, E., Council, O., Ping, L., Faison, E. M., Prabhu, S. S., Potter, E. L., Upton, S. L., Yin, G., Fay, J. M., Kincer, L. P., Spielvogel, E., Campbell, S. L., Benhabbour, S. R., Ke, H., Swanstrom, R. & Dokholyan, N., Dec 1 2019, In : Nature communications. 10, 1, 948.

Research output: Contribution to journalArticle

human immunodeficiency virus
carbohydrates
antibodies
HIV-1
Epitopes
7 Citations (Scopus)

RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells

Ke, W., Hong, E., Saito, R. F., Rangel, M. C., Wang, J., Viard, M., Richardson, M., Khisamutdinov, E. F., Panigaj, M., Dokholyan, N., Chammas, R., Dobrovolskaia, M. A. & Afonin, K. A., Jan 1 2019, In : Nucleic acids research. 47, 3, p. 1350-1361 12 p.

Research output: Contribution to journalArticle

Open Access
RNA Interference
Nucleic Acids
RNA
DNA
Biosensing Techniques

Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling

Zhu, C., Han, Q., Samoshkin, A., Convertino, M., Linton, A., Faison, E. M., Ji, R. R., Diatchenko, L. & Dokholyan, N. V., Oct 1 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 10, p. 878-884 7 p.

Research output: Contribution to journalArticle

Opioid Receptors
Morphine
Stabilization
Signal transduction
Mutation
1 Citation (Scopus)

Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding

Reilley, D. J., Popov, K. I., Dokholyan, N. V. & Alexandrova, A. N., May 30 2019, In : Journal of Physical Chemistry B. 123, 21, p. 4534-4539 6 p.

Research output: Contribution to journalArticle

Phenylalanine Hydroxylase
phenylalanine
Molecular dynamics
Enzymes
Iron
2 Citations (Scopus)

Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon

Li, X., Deng, M., Petrucelli, A. S., Zhu, C., Mo, J., Zhang, L., Tam, J. W., Ariel, P., Zhao, B., Zhang, S., Ke, H., Li, P., Dokholyan, N., Duncan, J. A. & Ting, J. P. Y., Mar 19 2019, In : Immunity. 50, 3, p. 591-599.e6

Research output: Contribution to journalArticle

Interferon alpha-beta Receptor
Viral DNA
Nucleic Acids
Interferons
Interferon Type I

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology

Proctor, E. A., Mowrey, D. D. & Dokholyan, N., Jul 1 2019, In : PLoS computational biology. 15, 7, e1007225.

Research output: Contribution to journalArticle

Open Access
etiology
Amyotrophic Lateral Sclerosis
Alanine
alanine
serine
2018
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
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
2 Citations (Scopus)

G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to ytosolic and luminal Ca2+

Xu, L., Mowrey, D. D., Chirasani, V. R., Wang, Y., Pasek, D. A., Dokholyan, N. V. & Meissner, G., Jan 1 2018, In : Journal of Biological Chemistry. 293, 6, p. 2015-2028 14 p.

Research output: Contribution to journalArticle

S 6
Ryanodine Receptor Calcium Release Channel
Linings
Muscle
Skeletal Muscle
13 Citations (Scopus)

High-speed atomic force microscopy reveals structural dynamics of α -synuclein monomers and dimers

Zhang, Y., Hashemi, M., Lv, Z., Williams, B., Popov, K. I., Dokholyan, N. V. & Lyubchenko, Y. L., Mar 28 2018, In : Journal of Chemical Physics. 148, 12, 123322.

Research output: Contribution to journalArticle

Synucleins
dynamic structural analysis
Structural dynamics
Dimers
Atomic force microscopy
10 Citations (Scopus)

Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis

Zhu, C., Beck, M. V., Griffith, J. D., Deshmukh, M. & Dokholyan, N. V., May 1 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 18, p. 4661-4665 5 p.

Research output: Contribution to journalArticle

Amyotrophic Lateral Sclerosis
Cell Survival
Motor Neurons
Poisons
Neurodegenerative Diseases
1 Citation (Scopus)

Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator

Wang, C., Aleksandrov, A. A., Yang, Z., Forouhar, F., Proctor, E. A., Kota, P., An, J., Kaplan, A., Khazanov, N., Boël, G., Stockwell, B. R., Senderowitz, H., Dokholyan, N. V., Riordan, J. R., Brouillette, C. G. & Hunt, J. F., Jan 1 2018, In : Journal of Biological Chemistry. 293, 46, p. 17685-17704 20 p.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Ligands
Mutation
Nucleotides
Molecules

Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel

Shobair, M., Popov, K. I., Dang, Y. L., He, H., Jackson Stutts, M. & Dokholyan, N. V., Jan 1 2018, In : Journal of Biological Chemistry. 293, 10, p. 3675-3684 10 p.

Research output: Contribution to journalArticle

Epithelial Sodium Channels
Chromosome Mapping
Degenerin Sodium Channels
Cysteine
Chemical activation
8 Citations (Scopus)

miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus

Han, Q., Liu, D., Convertino, M., Wang, Z., Jiang, C., Kim, Y. H., Luo, X., Zhang, X., Nackley, A., Dokholyan, N. & Ji, R. R., Aug 8 2018, In : Neuron. 99, 3, p. 449-463.e6

Research output: Contribution to journalArticle

Pruritus
MicroRNAs
Lymphoma
Ion Channels
S 6
5 Citations (Scopus)

P62-dependent phase separation of patient-derived KEap1 mutations and Nrf2

Cloer, E. W., Siesser, P. F., Cousins, E. M., Goldfarb, D., Mowrey, D. D., Harrison, J. S., Weir, S. J., Dokholyan, N. & Major, M. B., Nov 1 2018, In : Molecular and cellular biology. 38, 22, e0064417.

Research output: Contribution to journalArticle

Mutation
Polyubiquitin
Phenotype
Autophagy
Molecular Dynamics Simulation
9 Citations (Scopus)

Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells

Luo, J., Samanta, S., Convertino, M., Dokholyan, N. & Deiters, A., Oct 18 2018, In : ChemBioChem. 19, 20, p. 2178-2185 8 p.

Research output: Contribution to journalArticle

Cells
Amino Acids
Firefly Luciferases
Biological Phenomena
Light
12 Citations (Scopus)

RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition

Rackley, L., Stewart, J. M., Salotti, J., Krokhotin, A., Shah, A., Halman, J. R., Juneja, R., Smollett, J., Lee, L., Roark, K., Viard, M., Tarannum, M., Vivero-Escoto, J., Johnson, P. F., Dobrovolskaia, M. A., Dokholyan, N., Franco, E. & Afonin, K. A., Nov 28 2018, In : Advanced Functional Materials. 28, 48, 1805959.

Research output: Contribution to journalArticle

RNA
Small Interfering RNA
fibers
Fibers
engineers
6 Citations (Scopus)

Structural complexity and functional diversity of plant NADPH oxidases

Kaur, G., Guruprasad, K., Temple, B. R. S., Shirvanyants, D. G., Dokholyan, N. & Pati, P. K., Jan 1 2018, In : Amino Acids. 50, 1, p. 79-94 16 p.

Research output: Contribution to journalArticle

NADPH Oxidase
Plant Structures
Gene Duplication
Protein Folding
Molecular Dynamics Simulation
7 Citations (Scopus)

Tyrosine phosphorylation switching of a G protein

Li, B., Tunc-Ozdemir, M., Urano, D., Jia, H., Werth, E. G., Mowrey, D. D., Hicks, L. M., Dokholyan, N. V., Torres, M. P. & Jones, A. M., Jan 1 2018, In : Journal of Biological Chemistry. 293, 13, p. 4752-4766 15 p.

Research output: Contribution to journalArticle

Phosphorylation
GTP Phosphohydrolases
GTP-Binding Proteins
Tyrosine
GTP-Binding Protein Regulators
2017
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
10 Citations (Scopus)

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

Woods, C. T., Lackey, L., Williams, B., Dokholyan, N., 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
5 Citations (Scopus)

Computational protein design through grafting and stabilization

Zhu, C., Mowrey, D. D. & Dokholyan, N., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 227-241 15 p. (Methods in Molecular Biology; vol. 1529).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutation
Proteins
Protein Stability
Software
Databases
1 Citation (Scopus)

Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

Jacob, R. B., Michaels, K. C., Anderson, C. J., Fay, J. M. & Dokholyan, N. V., Apr 28 2017, In : Scientific reports. 7, 1 p.

Research output: Contribution to journalComment/debate

Open Access
10 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

Nucleotides
RNA
Base Pairing
8 Citations (Scopus)

Engineering Pak1 Allosteric Switches

Dagliyan, O., Karginov, A. V., Yagishita, S., Gale, M. E., Wang, H., Dermardirossian, C., Wells, C. M., Dokholyan, N. V., Kasai, H. & Hahn, K. M., Jul 21 2017, In : ACS Synthetic Biology. 6, 7, p. 1257-1262 6 p.

Research output: Contribution to journalArticle

p21-Activated Kinases
Sirolimus
Chemical activation
Switches
Graph theory
4 Citations (Scopus)

Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor

Mowrey, D. D., Xu, L., Mei, Y., Pasek, D. A., Meissner, G. & Dokholyan, N. V., Jan 1 2017, In : Journal of Biological Chemistry. 292, 31, p. 12947-12958 12 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Muscle
Skeletal Muscle
Ions
Constriction
1 Citation (Scopus)

Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue

Williams, B., Convertino, M., Das, J. & Dokholyan, N., Nov 21 2017, In : Biophysical journal. 113, 10, p. 2192-2198 7 p.

Research output: Contribution to journalArticle

Apolipoprotein E4
Mutation
Alzheimer Disease
Apolipoprotein E2
Apolipoprotein E3
29 Citations (Scopus)

Physicochemical code for quinary protein interactions in Escherichia coli

Mu, X., Choi, S., Lang, L., Mowray, D., Dokholyan, N. V., Danielsson, J. & Oliveberg, M., Jun 6 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 23, p. E4556-E4563

Research output: Contribution to journalArticle

Escherichia coli
Proteins
Bacterial Proteins
Escherichia coli Proteins
Hydrophobic and Hydrophilic Interactions
16 Citations (Scopus)

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene

Dakal, T. C., Kala, D., Dhiman, G., Yadav, V., Krokhotin, A. & Dokholyan, N., Dec 1 2017, In : Scientific reports. 7, 1, 6525.

Research output: Contribution to journalArticle

Interleukin-8
Single Nucleotide Polymorphism
Genes
Sequence Homology
Amino Acid Substitution
2 Citations (Scopus)
Protein folding
protein folding
Protein Folding
folding
proteins
3 Citations (Scopus)

Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition

Dronamraju, R., Ramachandran, S., Jha, D. K., Adams, A. T., Difiore, J. V., Parra, M. A., Dokholyan, N. V. & Strahl, B. D., Dec 1 2017, In : Scientific reports. 7, 1, 10791.

Research output: Contribution to journalArticle

Heterochromatin
Histone Chaperones
Molecular Dynamics Simulation
Histones
DNA Damage
50 Citations (Scopus)

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao, Z., Adamiak, R. W., Antczak, M., Batey, R. T., Becka, A. J., Biesiada, M., Boniecki, M. J., Bujnicki, J. M., Chen, S. J., Cheng, C. Y., Chou, F. C., Ferré-D'Amaré, A. R., Das, R., Dawson, W. K., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Geniesse, C., Kappel, K., Kladwang, W. & 26 others, Krokhotin, A., Łach, G. E., Major, F., Mann, T. H., Magnus, M., Pachulska-Wieczorek, K., Patel, D. J., Piccirilli, J. A., Popenda, M., Purzycka, K. J., Ren, A., Rice, G. M., Santalucia, J., Sarzynska, J., Szachniuk, M., Tandon, A., Trausch, J. J., Tian, S., Wang, J., Weeks, K. M., Williams, B., Xiao, Y., Xu, X., Zhang, D., Zok, T. & Westhof, E., May 2017, In : RNA. 23, 5, p. 655-672 18 p.

Research output: Contribution to journalArticle

Riboswitch
Catalytic RNA
RNA
Ligands
Glutamine
23 Citations (Scopus)

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

Brodie, N. I., Popov, K. I., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Jul 5 2017, In : Science Advances. 3, 7, e1700479.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Tacrolimus Binding Proteins
Proteins
Myoglobin
Deuterium
4 Citations (Scopus)

Structure modeling of RNA using sparse NMR constraints

Williams, B., Zhao, B., Tandon, A., Ding, F., Weeks, K. M., Zhang, Q. & Dokholyan, N. V., Dec 15 2017, In : Nucleic acids research. 45, 22, p. 12638-12647 10 p.

Research output: Contribution to journalArticle

RNA
Molecular Dynamics Simulation
Molecular Conformation
Benchmarking
Nucleotide Motifs
7 Citations (Scopus)

Transmembrane helical interactions in the CFTR channel pore

Das, J., Aleksandrov, A. A., Cui, L., He, L., Riordan, J. R. & Dokholyan, N. V., Jun 2017, In : PLoS computational biology. 13, 6, e1005594.

Research output: Contribution to journalArticle

Fibrosis
Cystic Fibrosis Transmembrane Conductance Regulator
cystic fibrosis
Conductance
Regulator
2016
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