Researcher Profile

Researcher Profile

Nikolay Dokholyan, PhD, MS

Nikolay Dokholyan, PhD, MS

G. Thomas Passananti Professor and Vice Chair for Research, Department of Pharmacology
G. Thomas Passananti Professor, Department of Biochemistry and Molecular Biology
Scientific Program:Experimental Therapeutics
nxd338@psu.edu

Research Interests

The mission of Dr. Nikolay Dokholyan's laboratory is to develop and apply integrated computational and experimental strategies to understand, sense and control misfolded proteins in order to uncover the etiologies of human neurodegenerative diseases and develop therapeutics to fight them.

The lab aims to understand the molecular disease mechanisms of ALS: How does the misfolding of superoxide dismutase (SOD1) lead to the formation of toxic oligomeric intermediates? Using biochemical and biophysical approaches and innovative computation, the Dokholyan lab determined putative structures of SOD1 oligomers and is currently elucidating the downstream pathways that lead to motorneuron death. Structures of toxic oligomers provide targets for drug discovery, which the lab is pursuing.

Neurodegenerative diseases such as ALS, Alzheimer’s, Huntington’s, Parkinson’s and prion diseases share similar processes associated with protein misfolding and aggregation. These similarities suggest common pathways leading to neuron death that eventually result in a disease. The lab is working toward understanding the general principles of protein misfolding in neurodegenerative diseases through computational and experimental approaches.

To sense and control protein conformations, the lab is working toward development of genetically-encoded proteins that bind and report rare/intermediate conformations of target molecules or alter their state using drugs or light.

One of the critical components of the lab's integrative research is drug discovery, focusing on both biological therapeutics and small molecule screening. The lab developed a fully flexible docking algorithm, MedusaDock, that allows for virtual screening of compounds and is is an important asset for small molecule drug discovery efforts.

The lab has developed novel approaches to molecular dynamics simulations and modeling, allowing studies of biological molecules at time scales relevant to biological systems. These approaches synergistically integrate rapid dynamics simulations, molecular modeling and design, and biochemical and cellular biology experiments, allowing for significant strides in understanding the etiology of misfolding diseases.

  • Proteins
  • Molecular Dynamics Simulation
  • Mutation
  • RNA
  • Ligands
  • Thermodynamics
  • Protein Folding
  • DNA
  • Cystic Fibrosis Transmembrane Conductance Regulator
  • Amyotrophic Lateral Sclerosis
  • Peptides
  • Ryanodine Receptor Calcium Release Channel

Recent Publications

2019

Wodak, SJ, Paci, E, Dokholyan, N, Berezovsky, IN, Horovitz, A, Li, J, Hilser, VJ, Bahar, I, Karanicolas, J, Stock, G, Hamm, P, Stote, RH, Eberhardt, J, Chebaro, Y, Dejaegere, A, Cecchini, M, Changeux, JP, Bolhuis, PG, Vreede, J, Faccioli, P, Orioli, S, Ravasio, R, Yan, L, Brito, C, Wyart, M, Gkeka, P, Rivalta, I, Palermo, G, McCammon, JA, Panecka-Hofman, J, Wade, RC, Di Pizio, A, Niv, MY, Nussinov, R, Tsai, CJ, Jang, H, Padhorny, D, Kozakov, D & McLeish, T 2019, 'Allostery in Its Many Disguises: From Theory to Applications', Structure, vol. 27, no. 4, pp. 566-578. https://doi.org/10.1016/j.str.2019.01.003
Sarker, M, Lee, HT, Mei, L, Krokhotin, A, de los Reyes, SE, Yen, L, Costantini, LM, Griffith, J, Dokholyan, N, Alushin, GM & Campbell, SL 2019, 'Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies' Journal of Molecular Biology, vol. 431, no. 8, pp. 1604-1618. https://doi.org/10.1016/j.jmb.2019.02.024
Brodie, NI, Popov, KI, Petrotchenko, EV, Dokholyan, N & Borchers, CH 2019, 'Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations' PLoS computational biology, vol. 15, no. 3, e1006859. https://doi.org/10.1371/journal.pcbi.1006859
Dagliyan, O, Dokholyan, N & Hahn, KM 2019, 'Engineering proteins for allosteric control by light or ligands' Nature Protocols, vol. 14, no. 6, pp. 1863-1883. https://doi.org/10.1038/s41596-019-0165-3
Wang, J, Williams, B, Chirasani, VR, Krokhotin, A, Das, R & Dokholyan, N 2019, 'Limits in accuracy and a strategy of RNA structure prediction using experimental information', Nucleic acids research, vol. 47, no. 11, pp. 5563-5572. https://doi.org/10.1093/nar/gkz427
Jiang, Y, Zhang, Y, Leung, JY, Fan, C, Popov, KI, Su, S, Qian, J, Wang, X, Holtzhausen, A, Ubil, E, Xiang, Y, Davis, I, Dokholyan, N, Wu, G, Perou, CM, Kim, WY, Earp, HS & Liu, P 2019, 'MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression', Nature communications, vol. 10, no. 1, 1515. https://doi.org/10.1038/s41467-019-09233-7
Wang, J & Dokholyan, N 2019, 'MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking with Constraints' Journal of Chemical Information and Modeling, vol. 59, no. 6, pp. 2509-2515. https://doi.org/10.1021/acs.jcim.8b00905
Bonfanti, S, Lionetti, MC, Fumagalli, MR, Chirasani, VR, Tiana, G, Dokholyan, N, Zapperi, S & La Porta, CAM 2019, 'Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins' Scientific reports, vol. 9, no. 1, 7615. https://doi.org/10.1038/s41598-019-44151-0
Ke, W, Hong, E, Saito, RF, Rangel, MC, Wang, J, Viard, M, Richardson, M, Khisamutdinov, EF, Panigaj, M, Dokholyan, N, Chammas, R, Dobrovolskaia, MA & Afonin, KA 2019, 'RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells', Nucleic acids research, vol. 47, no. 3, pp. 1350-1361. https://doi.org/10.1093/nar/gky1215
Zhu, C, Dukhovlinova, E, Council, O, Ping, L, Faison, EM, Prabhu, SS, Potter, EL, Upton, SL, Yin, G, Fay, JM, Kincer, LP, Spielvogel, E, Campbell, SL, Benhabbour, SR, Ke, H, Swanstrom, R & Dokholyan, N 2019, 'Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies' Nature communications, vol. 10, no. 1, 948. https://doi.org/10.1038/s41467-019-08876-w
Zhu, C, Han, Q, Samoshkin, A, Convertino, M, Linton, A, Faison, EM, Ji, RR, Diatchenko, L & Dokholyan, N 2019, 'Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling', Proteins: Structure, Function and Bioinformatics. https://doi.org/10.1002/prot.25751
Reilley, DJ, Popov, KI, Dokholyan, N & Alexandrova, AN 2019, 'Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding' Journal of Physical Chemistry B, vol. 123, no. 21, pp. 4534-4539. https://doi.org/10.1021/acs.jpcb.9b02893
Li, X, Deng, M, Petrucelli, AS, Zhu, C, Mo, J, Zhang, L, Tam, JW, Ariel, P, Zhao, B, Zhang, S, Ke, H, Li, P, Dokholyan, N, Duncan, JA & Ting, JPY 2019, 'Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon', Immunity, vol. 50, no. 3, pp. 591-599.e6. https://doi.org/10.1016/j.immuni.2019.02.009

2018

Xu, L, Chirasani, VR, Carter, JS, Pasek, DA, Dokholyan, N, Yamaguchi, N & Meissner, G 2018, ' Ca 2 -mediated activation of the skeletal-muscle ryanodine receptor ion channel ', Journal of Biological Chemistry, vol. 293, no. 50, pp. 19501-19509. https://doi.org/10.1074/jbc.RA118.004453
Xu, L, Mowrey, DD, Chirasani, VR, Wang, Y, Pasek, DA, Dokholyan, N & Meissner, G 2018, ' G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to ytosolic and luminal Ca 2+ ', Journal of Biological Chemistry, vol. 293, no. 6, pp. 2015-2028. https://doi.org/10.1074/jbc.M117.803247
Dagliyan, O, Krokhotin, A, Ozkan-Dagliyan, I, Deiters, A, Der, CJ, Hahn, KM & Dokholyan, N 2018, 'Computational design of chemogenetic and optogenetic split proteins', Nature communications, vol. 9, no. 1, 4042. https://doi.org/10.1038/s41467-018-06531-4
Zhang, Y, Hashemi, M, Lv, Z, Williams, B, Popov, KI, Dokholyan, N & Lyubchenko, YL 2018, 'High-speed atomic force microscopy reveals structural dynamics of α -synuclein monomers and dimers', Journal of Chemical Physics, vol. 148, no. 12, 123322. https://doi.org/10.1063/1.5008874
Zhu, C, Beck, MV, Griffith, JD, Deshmukh, M & Dokholyan, N 2018, 'Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis', Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 18, pp. 4661-4665. https://doi.org/10.1073/pnas.1800187115
Wang, C, Aleksandrov, AA, Yang, Z, Forouhar, F, Proctor, EA, Kota, P, An, J, Kaplan, A, Khazanov, N, Boël, G, Stockwell, BR, Senderowitz, H, Dokholyan, N, Riordan, JR, Brouillette, CG & Hunt, JF 2018, 'Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator', Journal of Biological Chemistry, vol. 293, no. 46, pp. 17685-17704. https://doi.org/10.1074/jbc.RA117.000819
Shobair, M, Popov, KI, Dang, YL, He, H, Jackson Stutts, M & Dokholyan, N 2018, 'Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel' Journal of Biological Chemistry, vol. 293, no. 10, pp. 3675-3684. https://doi.org/10.1074/jbc.RA117.000604
Cloer, EW, Siesser, PF, Cousins, EM, Goldfarb, D, Mowrey, DD, Harrison, JS, Weir, SJ, Dokholyan, N & Major, MB 2018, 'P62-dependent phase separation of patient-derived KEap1 mutations and Nrf2', Molecular and cellular biology, vol. 38, no. 22, e0064417. https://doi.org/10.1128/MCB.00644-17
Rackley, L, Stewart, JM, Salotti, J, Krokhotin, A, Shah, A, Halman, JR, Juneja, R, Smollett, J, Lee, L, Roark, K, Viard, M, Tarannum, M, Vivero-Escoto, J, Johnson, PF, Dobrovolskaia, MA, Dokholyan, N, Franco, E & Afonin, KA 2018, 'RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition', Advanced Functional Materials, vol. 28, no. 48, 1805959. https://doi.org/10.1002/adfm.201805959
Luo, J, Samanta, S, Convertino, M, Dokholyan, N & Deiters, A 2018, 'Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells', ChemBioChem, vol. 19, no. 20, pp. 2178-2185. https://doi.org/10.1002/cbic.201800226
Kaur, G, Guruprasad, K, Temple, BRS, Shirvanyants, DG, Dokholyan, N & Pati, PK 2018, 'Structural complexity and functional diversity of plant NADPH oxidases', Amino Acids, vol. 50, no. 1, pp. 79-94. https://doi.org/10.1007/s00726-017-2491-5
Li, B, Tunc-Ozdemir, M, Urano, D, Jia, H, Werth, EG, Mowrey, DD, Hicks, LM, Dokholyan, N, Torres, MP & Jones, AM 2018, 'Tyrosine phosphorylation switching of a G protein', Journal of Biological Chemistry, vol. 293, no. 13, pp. 4752-4766. https://doi.org/10.1074/jbc.RA117.000163
Han, Q, Liu, D, Convertino, M, Wang, Z, Jiang, C, Kim, YH, Luo, X, Zhang, X, Nackley, A, Dokholyan, N & Ji, RR 2018, 'miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus', Neuron, vol. 99, no. 3, pp. 449-463.e6. https://doi.org/10.1016/j.neuron.2018.06.039

2017

Thompson, PM, Ramachandran, S, Case, LB, Tolbert, CE, Tandon, A, Pershad, M, Dokholyan, N, Waterman, CM & Campbell, SL 2017, 'A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization', Structure, vol. 25, no. 2, pp. 264-275. https://doi.org/10.1016/j.str.2016.12.002
Woods, CT, Lackey, L, Williams, B, Dokholyan, N, Gotz, D & Laederach, A 2017, 'Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo', Biophysical journal, vol. 113, no. 2, pp. 290-301. https://doi.org/10.1016/j.bpj.2017.05.031
Zhu, C, Mowrey, DD & Dokholyan, N 2017, Computational protein design through grafting and stabilization. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1529, Humana Press Inc., pp. 227-241. https://doi.org/10.1007/978-1-4939-6637-0_11
Krokhotin, A, Mustoe, AM, Weeks, KM & Dokholyan, N 2017, 'Direct identification of base-paired RNA nucleotides by correlated chemical probing', RNA, vol. 23, no. 1, pp. 6-13. https://doi.org/10.1261/rna.058586.116
Dagliyan, O, Karginov, AV, Yagishita, S, Gale, ME, Wang, H, Dermardirossian, C, Wells, CM, Dokholyan, N, Kasai, H & Hahn, KM 2017, 'Engineering Pak1 Allosteric Switches', ACS Synthetic Biology, vol. 6, no. 7, pp. 1257-1262. https://doi.org/10.1021/acssynbio.6b00359
Mowrey, DD, Xu, L, Mei, Y, Pasek, DA, Meissner, G & Dokholyan, N 2017, 'Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor', Journal of Biological Chemistry, vol. 292, no. 31, pp. 12947-12958. https://doi.org/10.1074/jbc.M116.760199
Williams, B, Convertino, M, Das, J & Dokholyan, N 2017, 'Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue', Biophysical journal, vol. 113, no. 10, pp. 2192-2198. https://doi.org/10.1016/j.bpj.2017.08.026
Mu, X, Choi, S, Lang, L, Mowray, D, Dokholyan, N, Danielsson, J & Oliveberg, M 2017, 'Physicochemical code for quinary protein interactions in Escherichia coli', Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 23, pp. E4556-E4563. https://doi.org/10.1073/pnas.1621227114
Dakal, TC, Kala, D, Dhiman, G, Yadav, V, Krokhotin, A & Dokholyan, N 2017, 'Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene', Scientific reports, vol. 7, no. 1, 6525. https://doi.org/10.1038/s41598-017-06575-4
Krokhotin, A & Dokholyan, N 2017, 'Protein folding: Over half a century lasting quest: Comment on “There and back again: Two views on the protein folding puzzle” by Alexei V. Finkelstein et al.', Physics of Life Reviews, vol. 21, pp. 72-74. https://doi.org/10.1016/j.plrev.2017.06.002
Miao, Z, Adamiak, RW, Antczak, M, Batey, RT, Becka, AJ, Biesiada, M, Boniecki, MJ, Bujnicki, JM, Chen, SJ, Cheng, CY, Chou, FC, Ferré-D'Amaré, AR, Das, R, Dawson, WK, Ding, F, Dokholyan, N, Dunin-Horkawicz, S, Geniesse, C, Kappel, K, Kladwang, W, Krokhotin, A, Łach, GE, Major, F, Mann, TH, Magnus, M, Pachulska-Wieczorek, K, Patel, DJ, Piccirilli, JA, Popenda, M, Purzycka, KJ, Ren, A, Rice, GM, Santalucia, J, Sarzynska, J, Szachniuk, M, Tandon, A, Trausch, JJ, Tian, S, Wang, J, Weeks, KM, Williams, B, Xiao, Y, Xu, X, Zhang, D, Zok, T & Westhof, E 2017, 'RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme', RNA, vol. 23, no. 5, pp. 655-672. https://doi.org/10.1261/rna.060368.116
Dronamraju, R, Ramachandran, S, Jha, DK, Adams, AT, Difiore, JV, Parra, MA, Dokholyan, N & Strahl, BD 2017, 'Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition', Scientific reports, vol. 7, no. 1, 10791. https://doi.org/10.1038/s41598-017-11003-8
Brodie, NI, Popov, KI, Petrotchenko, EV, Dokholyan, N & Borchers, CH 2017, 'Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations', Science Advances, vol. 3, no. 7, e1700479. https://doi.org/10.1126/sciadv.1700479
Williams, B, Zhao, B, Tandon, A, Ding, F, Weeks, KM, Zhang, Q & Dokholyan, N 2017, 'Structure modeling of RNA using sparse NMR constraints', Nucleic acids research, vol. 45, no. 22, pp. 12638-12647. https://doi.org/10.1093/nar/gkx1058
Das, J, Aleksandrov, AA, Cui, L, He, L, Riordan, JR & Dokholyan, N 2017, 'Transmembrane helical interactions in the CFTR channel pore', PLoS computational biology, vol. 13, no. 6, e1005594. https://doi.org/10.1371/journal.pcbi.1005594

2016

Fay, JM, Zhu, C, Proctor, EA, Tao, Y, Cui, W, Ke, H & Dokholyan, N 2016, 'A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation', Structure, vol. 24, no. 11, pp. 1898-1906. https://doi.org/10.1016/j.str.2016.08.011
Hadi-Alijanvand, H, Proctor, EA, Ding, F, Dokholyan, N & Moosavi-Movahedi, AA 2016, 'A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase', Proteins: Structure, Function and Bioinformatics, vol. 84, no. 5, pp. 611-623. https://doi.org/10.1002/prot.25011
Chandrasekaran, SN, Das, J, Dokholyan, N & Carter, CW 2016, 'A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms', Structural Dynamics, vol. 3, no. 1, 012101. https://doi.org/10.1063/1.4941599
Proctor, EA & Dokholyan, N 2016, 'Applications of Discrete Molecular Dynamics in biology and medicine', Current Opinion in Structural Biology, vol. 37, pp. 9-13. https://doi.org/10.1016/j.sbi.2015.11.001
Convertino, M & Dokholyan, N 2016, Computational modeling of small molecule ligand binding interactions and affinities. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1414, Humana Press Inc., pp. 23-32. https://doi.org/10.1007/978-1-4939-3569-7_2
Dokholyan, N 2016, 'Controlling Allosteric Networks in Proteins', Chemical Reviews, vol. 116, no. 11, pp. 6463-6487. https://doi.org/10.1021/acs.chemrev.5b00544
Politi, R, Convertino, M, Popov, K, Dokholyan, N & Tropsha, A 2016, 'Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification but Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise', Journal of Chemical Information and Modeling, vol. 56, no. 6, pp. 1032-1041. https://doi.org/10.1021/acs.jcim.5b00751
Allen, SE, Dokholyan, N & Bowers, AA 2016, 'Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications', ACS Chemical Biology, vol. 11, no. 1, pp. 10-24. https://doi.org/10.1021/acschembio.5b00663
Dagliyan, O, Tarnawski, M, Chu, PH, Shirvanyants, D, Schlichting, I, Dokholyan, N & Hahn, KM 2016, 'Engineering extrinsic disorder to control protein activity in living cells', Science, vol. 354, no. 6318, pp. 1441-1444. https://doi.org/10.1126/science.aah3404
Shobair, M, Dagliyan, O, Kota, P, Dang, YL, He, H, Stutts, MJ & Dokholyan, N 2016, 'Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit coupling', Journal of Biological Chemistry, vol. 291, no. 8, pp. 3682-3692. https://doi.org/10.1074/jbc.M115.678052
Jacob, RB, Michaels, KC, Anderson, CJ, Fay, JM & Dokholyan, N 2016, 'Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins' Scientific reports, vol. 6, 37175. https://doi.org/10.1038/srep37175
Proctor, EA, Fee, L, Tao, Y, Redler, RL, Fay, JM, Zhang, Y, Lv, Z, Mercer, IP, Deshmukh, M, Lyubchenko, YL & Dokholyan, N 2016, 'Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, no. 3, pp. 614-619. https://doi.org/10.1073/pnas.1516725113
Convertino, M, Das, J & Dokholyan, N 2016, 'Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases', ACS Chemical Biology, vol. 11, no. 6, pp. 1471-1489. https://doi.org/10.1021/acschembio.6b00195
Redler, RL, Das, J, Diaz, JR & Dokholyan, N 2016, 'Protein Destabilization as a Common Factor in Diverse Inherited Disorders', Journal Of Molecular Evolution, vol. 82, no. 1, pp. 11-16. https://doi.org/10.1007/s00239-015-9717-5
Gentzsch, M, Ren, HY, Houck, SA, Quinney, NL, Cholon, DM, Sopha, P, Chaudhry, IG, Das, J, Dokholyan, N, Randell, SH & Cyr, DM 2016, 'Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770', American Journal of Physiology - Lung Cellular and Molecular Physiology, vol. 311, no. 3, pp. L550-L559. https://doi.org/10.1152/ajplung.00186.2016

2015

Williams, B, Convertino, M, Das, J & Dokholyan, N 2015, 'ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations' PLoS computational biology, vol. 11, no. 10, e1004359. https://doi.org/10.1371/journal.pcbi.1004359
Meloto, CB, Segall, SK, Smith, S, Parisien, M, Shabalina, SA, Rizzatti-Barbosa, CM, Gauthier, J, Tsao, D, Convertino, M, Piltonen, MH, Slade, GD, Fillingim, RB, Greenspan, JD, Ohrbach, R, Knott, C, Maixner, W, Zaykin, D, Dokholyan, N, Reenila, I, Mannisto, PT & Diatchenko, L 2015, 'COMT gene locus: New functional variants', Pain, vol. 156, no. 10, pp. 2072-2083. https://doi.org/10.1097/j.pain.0000000000000273
Mei, Y, Xu, L, Mowrey, DD, Giraldez, RM, Wang, Y, Pasek, DA, Dokholyan, N & Meissner, G 2015, 'Channel gating dependence on pore lining helix glycine residues in skeletal muscle ryanodine receptor' Journal of Biological Chemistry, vol. 290, no. 28, pp. 17535-17545. https://doi.org/10.1074/jbc.M115.659672
Krokhotin, A & Dokholyan, N 2015, Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models. in Methods in Enzymology. Methods in Enzymology, vol. 553, Academic Press Inc., pp. 65-89. https://doi.org/10.1016/bs.mie.2014.10.052
Martin, LJ, Piltonen, MH, Gauthier, J, Convertino, M, Acland, EL, Dokholyan, N, Mogil, JS, Diatchenko, L & Maixner, W 2015, 'Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers', Journal of Pain, vol. 16, no. 12, pp. 1321-1333. https://doi.org/10.1016/j.jpain.2015.09.004
Convertino, M, Samoshkin, A, Viet, CT, Gauthier, J, Fraine, SPL, Sharif-Naeini, R, Schmidt, BL, Maixner, W, Diatchenko, L & Dokholyan, N 2015, 'Differential regulation of 6- and 7-Transmembrane helix variants of μ-opioid receptor in response to morphine stimulation', PloS one, vol. 10, no. 11, e0142826. https://doi.org/10.1371/journal.pone.0142826
Brown, KA, Zou, Y, Shirvanyants, D, Zhang, J, Samanta, S, Mantravadi, PK, Dokholyan, N & Deiters, A 2015, 'Light-cleavable rapamycin dimer as an optical trigger for protein dimerization' Chemical Communications, vol. 51, no. 26, pp. 5702-5705. https://doi.org/10.1039/c4cc09442e
Wang, L, Xie, L, Ramachandran, S, Lee, YY, Yan, Z, Zhou, L, Krajewski, K, Liu, F, Zhu, C, Chen, DJ, Strahl, BD, Jin, J, Dokholyan, N & Chen, X 2015, 'Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX', Chemistry and Biology, vol. 22, no. 7, 3066, pp. 849-861. https://doi.org/10.1016/j.chembiol.2015.05.014
Miao, Z, Adamiak, RW, Blanchet, MF, Boniecki, M, Bujnicki, JM, Chen, SJ, Cheng, C, Chojnowski, G, Chou, FC, Cordero, P, Cruz, JA, Ferré-D'Amaré, AR, Das, R, Ding, F, Dokholyan, N, Dunin-Horkawicz, S, Kladwang, W, Krokhotin, A, Lach, G, Magnus, M, Major, F, Mann, TH, Masquida, B, Matelska, D, Meyer, M, Peselis, A, Popenda, M, Purzycka, KJ, Serganov, A, Stasiewicz, J, Szachniuk, M, Tandon, A, Tian, S, Wang, J, Xiao, Y, Xu, X, Zhang, J, Zhao, P, Zok, T & Westhof, E 2015, 'RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures', RNA (New York, N.Y.), vol. 21, no. 6, pp. 1066-1084. https://doi.org/10.1261/rna.049502.114
Proctor, EA, Kota, P, Aleksandrov, AA, He, L, Riordan, JR & Dokholyan, N 2015, 'Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator', Chemical Science, vol. 6, no. 2, pp. 1237-1246. https://doi.org/10.1039/c4sc01320d
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