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Nikolay Dokholyan, PhD, MS

Nikolay Dokholyan, PhD, MS

G. Thomas Passananti Professor and Vice Chair for Research, Department of Pharmacology
Professor, Department of Biochemistry and Molecular Biology
Penn State Neuroscience Institute
Center for Cannabis and Natural Product Pharmaceuticals (CCNPP)
Scientific Program:Next-Generation Therapies
NXD338@psu.edu

Research Interests

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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
  • Ligands
  • Mutation
  • RNA
  • Amyotrophic Lateral Sclerosis
  • Peptides
  • Protein Folding
  • Superoxide Dismutase-1
  • Thermodynamics
  • Ryanodine Receptor Calcium Release Channel
  • DNA
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Recent Publications

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2024

Vishweshwaraiah, YL, Hnath, B, Wang, J, Chandler, M, Mukherjee, A, Yennawar, NH, Booker, SJ, Afonin, KA & Dokholyan, NV 2024, 'A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2', ACS Applied Bio Materials, vol. 7, no. 5, pp. 3238-3246. https://doi.org/10.1021/acsabm.4c00222
Raup-Konsavage, WM, Sepulveda, DE, Wang, J, Dokholyan, NV, Vrana, KE & Graziane, NM 2024, 'Antinociceptive Effects of Cannabichromene (CBC) in Mice: Insights from von Frey, Tail-Flick, Formalin, and Acetone Tests', Biomedicines, vol. 12, no. 1, 83. https://doi.org/10.3390/biomedicines12010083
Kundu, D, Ghosh, A, Ekambaram, S, Wang, J, Dokholyan, N & Ghosh, S 2024, Application of Quantum Tensor Networks for Protein Classification. in GLSVLSI 2024 - Proceedings of the Great Lakes Symposium on VLSI 2024. Proceedings of the ACM Great Lakes Symposium on VLSI, GLSVLSI, Association for Computing Machinery, pp. 132-137, 34th Great Lakes Symposium on VLSI 2024, GLSVLSI 2024, Clearwater, United States, 6/12/24. https://doi.org/10.1145/3649476.3658701
Avila, YI, Rebolledo, LP, Skelly, E, de Freitas Saito, R, Wei, H, Lilley, D, Stanley, RE, Hou, YM, Yang, H, Sztuba-Solinska, J, Chen, SJ, Dokholyan, NV, Tan, C, Li, SK, He, X, Zhang, X, Miles, W, Franco, E, Binzel, DW, Guo, P & Afonin, KA 2024, 'Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology', ACS Applied Bio Materials, vol. 7, no. 6, pp. 3587-3604. https://doi.org/10.1021/acsabm.4c00432
Sha, CM, Wang, J & Dokholyan, NV 2024, 'Differentiable rotamer sampling with molecular force fields', Briefings in bioinformatics, vol. 25, no. 1, slad183. https://doi.org/10.1093/bib/bbad456
Johnson, H, Singh, A, Raza, A, Sha, CM, Wang, J, Gowda, K, Shen, Z, Nair, H, Li, C, Dokholyan, NV, Narayan, S & Sharma, AK 2024, 'Identification of a Novel Protein Phosphatase 2A Activator, PPA24, as a Potential Therapeutic for FOLFOX-Resistant Colorectal Cancer', Journal of Medicinal Chemistry, vol. 67, no. 20, pp. 18070-18089. https://doi.org/10.1021/acs.jmedchem.4c01077
Rebolledo, LP, Ke, W, Cedrone, E, Wang, J, Majithia, K, Brittany Johnson, M, Dokholyan, NV, Dobrovolskaia, MA & Afonin, KA 2024, 'Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure−Activity Relationship and Mechanistic Insights', ACS Applied Materials and Interfaces, vol. 16, no. 7, pp. 8430-8441. https://doi.org/10.1021/acsami.3c17779
Gomari, MM, Arab, SS, Balalaie, S, Ramezanpour, S, Hosseini, A, Dokholyan, NV & Tarighi, P 2024, 'Rational peptide design for targeting cancer cell invasion', Proteins: Structure, Function and Bioinformatics, vol. 92, no. 1, pp. 76-95. https://doi.org/10.1002/prot.26580
Casado Gama, H, Amorós, MA, Andrade de Araújo, M, Sha, CM, Vieira, MPS, Torres, RGD, Souza, GF, Junkes, JA, Dokholyan, NV, Leite Góes Gitaí, D & Duzzioni, M 2024, 'Systematic review and meta-analysis of dysregulated microRNAs derived from liquid biopsies as biomarkers for amyotrophic lateral sclerosis', Non-coding RNA Research, vol. 9, no. 2, pp. 523-535. https://doi.org/10.1016/j.ncrna.2024.02.006

2023

Chen, J, Vishweshwaraiah, YL, Mailman, RB, Tabdanov, ED & Dokholyan, NV 2023, 'A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments', Science Advances, vol. 9, no. 21, eadg1062. https://doi.org/10.1126/sciadv.adg1062
Jain, A, Dokholyan, NV & Lee, AL 2023, 'Allosteric inactivation of an engineered optogenetic GTPase', Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 14, e2219254120. https://doi.org/10.1073/pnas.2219254120
Godbole, SS & Dokholyan, NV 2023, 'Allosteric regulation of kinase activity in living cells', eLife, vol. 12. https://doi.org/10.7554/eLife.90574
Reynolds, JA, Vishweshwaraiah, YL, Chirasani, VR, Pritchard, JR & Dokholyan, NV 2023, 'An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity', Journal of Biological Chemistry, vol. 299, no. 4, 103069. https://doi.org/10.1016/j.jbc.2023.103069
Hnath, B, Chen, J, Reynolds, J, Choi, E, Wang, J, Zhang, D, Sha, CM & Dokholyan, NV 2023, 'Big versus small: The impact of aggregate size in disease', Protein Science, vol. 32, no. 7, e4686. https://doi.org/10.1002/pro.4686
Beasock, D, Ha, A, Halman, J, Panigaj, M, Wang, J, Dokholyan, NV & Afonin, KA 2023, 'Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs) via Enzymatic Degradation', Bioconjugate Chemistry, vol. 34, no. 6, pp. 1139-1146. https://doi.org/10.1021/acs.bioconjchem.3c00167
Wang, J, Sha, CM & Dokholyan, NV 2023, Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 2709, Humana Press Inc., pp. 51-64. https://doi.org/10.1007/978-1-0716-3417-2_3
Lawanprasert, A, Sloand, JN, González Vargas, M, Singh, H, Eldor, T, Miller, MA, Pimcharoen, S, Wang, J, Leighow, SM, Pritchard, JR, Dokholyan, NV & Medina, SH 2023, 'Deciphering the Mechanistic Basis for Perfluoroalkyl-Protein Interactions', ChemBioChem, vol. 24, no. 13, e202300159. https://doi.org/10.1002/cbic.202300159
Afonin, KA & Dokholyan, NV 2023, 'Editorial to “Molecular engineering of biomaterials programmed to operate in living systems”', Advanced Drug Delivery Reviews, vol. 193, 114669. https://doi.org/10.1016/j.addr.2022.114669
Chandrasekaran, SN, Das, J, Dokholyan, NV & Carter, CW 2023, 'Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase', Structural Dynamics, vol. 10, no. 4, 044301. https://doi.org/10.1063/4.0000181
Chirasani, VR, Khan, MAI, Malavade, JN, Dokholyan, NV, Hoffman, BD & Campbell, SL 2023, 'Molecular basis and cellular functions of vinculin-actin directional catch bonding', Nature communications, vol. 14, no. 1, 8300. https://doi.org/10.1038/s41467-023-43779-x
Sha, CM, Wang, J & Dokholyan, NV 2024, 'Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks', Biophysical journal, vol. 123, no. 17, pp. 2671-2681. https://doi.org/10.1016/j.bpj.2023.10.011
Fang, X, Liu, X, Chinchilli, VM, Wang, M, Wang, HG, Dokholyan, NV, Shen, C, Lee, JJ & Zhou, S 2023, 'REAP-2: An interactive quantitative tool for robust and efficient dose-response curve estimation', Journal of Clinical and Translational Science, vol. 7, no. 1, e219. https://doi.org/10.1017/cts.2023.642
Zamel, J, Chen, J, Zaer, S, Harris, PD, Drori, P, Lebendiker, M, Kalisman, N, Dokholyan, NV & Lerner, E 2023, 'Structural and dynamic insights into α-synuclein dimer conformations', Structure, vol. 31, no. 4, pp. 411-423.e6. https://doi.org/10.1016/j.str.2023.01.011
Chandrasekaran, B, Tyagi, A, Saran, U, Kolluru, V, Baby, BV, Chirasani, VR, Dokholyan, NV, Lin, JM, Singh, A, Sharma, AK, Ankem, MK & Damodaran, C 2023, 'Urolithin A analog inhibits castration-resistant prostate cancer by targeting the androgen receptor and its variant, androgen receptor-variant 7', Frontiers in Pharmacology, vol. 14, 1137783. https://doi.org/10.3389/fphar.2023.1137783
Khazan, N, Quarato, ER, Singh, NA, Snyder, CWA, Moore, T, Miller, JP, Yasui, M, Teramoto, Y, Goto, T, Reshi, S, Hong, J, Zhang, N, Pandey, D, Srivastava, P, Morell, A, Kawano, H, Kawano, Y, Conley, T, Sahasrabudhe, DM, Yano, N, Miyamoto, H, Aljitawi, O, Liesveld, J, Becker, MW, Calvi, LM, Zhovmer, AS, Tabdanov, ED, Dokholyan, NV, Linehan, DC, Hansen, JN, Gerber, SA, Sharon, A, Khera, MK, Jurutka, PW, Rochel, N, Kim, KK, Rowswell-Turner, RB, Singh, RK & Moore, RG 2023, 'Vitamin D Receptor Antagonist MeTC7 Inhibits PD-L1', Cancers, vol. 15, no. 13, 3432. https://doi.org/10.3390/cancers15133432

2022

Miller, WP, Sha, CM, Sunilkumar, S, Toro, AL, Vancleave, AM, Kimball, SR, Dokholyan, NV & Dennis, MD 2022, 'Activation of Disulfide Redox Switch in REDD1 Promotes Oxidative Stress Under Hyperglycemic Conditions', Diabetes, vol. 71, no. 12, pp. 2764-2776. https://doi.org/10.2337/db22-0355
Vishweshwaraiah, YL, Hnath, B, Rackley, B, Wang, J, Gontu, A, Chandler, M, Afonin, KA, Kuchipudi, SV, Christensen, N, Yennawar, NH & Dokholyan, NV 2022, 'Adaptation-Proof SARS-CoV-2 Vaccine Design', Advanced Functional Materials, vol. 32, no. 49, 2206055. https://doi.org/10.1002/adfm.202206055
Binder, JL, Berendzen, J, Stevens, AO, He, Y, Wang, J, Dokholyan, NV & Oprea, TI 2022, 'AlphaFold illuminates half of the dark human proteins', Current Opinion in Structural Biology, vol. 74, 102372. https://doi.org/10.1016/j.sbi.2022.102372
Tran, AN, Chandler, M, Halman, J, Beasock, D, Fessler, A, McKeough, RQ, Lam, PA, Furr, DP, Wang, J, Cedrone, E, Dobrovolskaia, MA, Dokholyan, NV, Trammell, SR & Afonin, KA 2022, 'Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures', Small, vol. 18, no. 13, 2104814. https://doi.org/10.1002/smll.202104814
Dokholyan, NV, Mohs, RC & Bateman, RJ 2022, 'Challenges and progress in research, diagnostics, and therapeutics in Alzheimer's disease and related dementias', Alzheimer's and Dementia: Translational Research and Clinical Interventions, vol. 8, no. 1, e12330. https://doi.org/10.1002/trc2.12330
Chen, J, Vishweshwaraiah, YL & Dokholyan, NV 2022, 'Design and engineering of allosteric communications in proteins', Current Opinion in Structural Biology, vol. 73, 102334. https://doi.org/10.1016/j.sbi.2022.102334
Yang, Y, Lewis, MM, Huang, X, Dokholyan, NV & Mailman, RB 2022, 'Dopamine D1 receptor-mediated β-arrestin signaling: Insight from pharmacology, biology, behavior, and neurophysiology', International Journal of Biochemistry and Cell Biology, vol. 148, 106235. https://doi.org/10.1016/j.biocel.2022.106235
Gomari, MM, Rostami, N, Faradonbeh, DR, Asemaneh, HR, Esmailnia, G, Arab, S, Farsimadan, M, Hosseini, A & Dokholyan, NV 2022, 'Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation', Proteins: Structure, Function and Bioinformatics, vol. 90, no. 11, pp. 1908-1925. https://doi.org/10.1002/prot.26386
Ke, W, Chandler, M, Cedrone, E, Saito, RF, Rangel, MC, De Souza Junqueira, M, Wang, J, Shi, D, Truong, N, Richardson, M, Rolband, LA, Dréau, D, Bedocs, P, Chammas, R, Dokholyan, NV, Dobrovolskaia, MA & Afonin, KA 2022, 'Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo', Nano letters, vol. 22, no. 14, pp. 5961-5972. https://doi.org/10.1021/acs.nanolett.2c02019
Zhang, DY, Wang, J, Fleeman, RM, Kuhn, MK, Swulius, MT, Proctor, EA & Dokholyan, NV 2022, 'Monosialotetrahexosylganglioside Promotes Early Aβ42 Oligomer Formation and Maintenance', ACS Chemical Neuroscience, vol. 13, no. 13, pp. 1979-1991. https://doi.org/10.1021/acschemneuro.2c00221
Amorós, MA, Choi, ES, Cofré, AR, Dokholyan, NV & Duzzioni, M 2022, 'Motor neuron-derived induced pluripotent stem cells as a drug screening platform for amyotrophic lateral sclerosis', Frontiers in Cell and Developmental Biology, vol. 10, 962881. https://doi.org/10.3389/fcell.2022.962881
Sha, CM, Wang, J & Dokholyan, NV 2022, 'NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules', Frontiers in Molecular Biosciences, vol. 9, 867241. https://doi.org/10.3389/fmolb.2022.867241
Gomari, MM, Abkhiz, S, Pour, TG, Lotfi, E, Rostami, N, Monfared, FN, Ghobari, B, Mosavi, M, Alipour, B & Dokholyan, NV 2022, 'Peptidomimetics in cancer targeting', Molecular Medicine, vol. 28, no. 1, 146. https://doi.org/10.1186/s10020-022-00577-3
Jiang, H, Wang, J, Cong, W, Huang, Y, Ramezani, M, Sarma, A, Dokholyan, NV, Mahdavi, M & Kandemir, MT 2022, 'Predicting Protein-Ligand Docking Structure with Graph Neural Network', Journal of Chemical Information and Modeling, vol. 62, no. 12, pp. 2923-2932. https://doi.org/10.1021/acs.jcim.2c00127
Zhou, S, Liu, X, Fang, X, Chinchilli, VM, Wang, M, Wang, HG, Dokholyan, NV, Shen, C & Lee, JJ 2022, 'Robust and Efficient Assessment of Potency (REAP) as a quantitative tool for dose-response curve estimation', eLife, vol. 11, e78634. https://doi.org/10.7554/eLife.78634
Gomari, MM, Tarighi, P, Choupani, E, Abkhiz, S, Mohamadzadeh, M, Rostami, N, Sadroddiny, E, Baammi, S, Uversky, VN & Dokholyan, NV 2023, 'Structural evolution of Delta lineage of SARS-CoV-2', International Journal of Biological Macromolecules, vol. 226, pp. 1116-1140. https://doi.org/10.1016/j.ijbiomac.2022.11.227
Vishweshwaraiah, YL & Dokholyan, NV 2022, 'Toward rational vaccine engineering', Advanced Drug Delivery Reviews, vol. 183, 114142. https://doi.org/10.1016/j.addr.2022.114142
Hnath, B & Dokholyan, NV 2022, 'Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS', Biophysical journal, vol. 121, no. 11, pp. 2084-2095. https://doi.org/10.1016/j.bpj.2022.04.037
Wang, J & Dokholyan, NV 2022, 'Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction', Journal of Chemical Information and Modeling, vol. 62, no. 3, pp. 463-471. https://doi.org/10.1021/acs.jcim.1c01531
Vishweshwaraiah, YL & Dokholyan, NV 2022, 'mRNA vaccines for cancer immunotherapy', Frontiers in immunology, vol. 13, 1029069. https://doi.org/10.3389/fimmu.2022.1029069

2021

Chen, YC, Dinavahi, SS, Feng, Q, Gowda, R, Ramisetti, S, Xia, X, LaPenna, KB, Chirasani, VR, Cho, SH, Hafenstein, SL, Battu, MB, Berg, A, Sharma, AK, Kirchhausen, T, Dokholyan, NV, Amin, S, He, P & Robertson, GP 2021, 'Activating Sphingosine-1-phospahte signaling in endothelial cells increases myosin light chain phosphorylation to decrease endothelial permeability thereby inhibiting cancer metastasis', Cancer Letters, vol. 506, pp. 107-119. https://doi.org/10.1016/j.canlet.2021.01.004
Nguyen, PH, Ramamoorthy, A, Sahoo, BR, Zheng, J, Faller, P, Straub, JE, Dominguez, L, Shea, JE, Dokholyan, NV, de Simone, A, Ma, B, Nussinov, R, Najafi, S, Ngo, ST, Loquet, A, Chiricotto, M, Ganguly, P, McCarty, J, Li, MS, Hall, C, Wang, Y, Miller, Y, Melchionna, S, Habenstein, B, Timr, S, Chen, J, Hnath, B, Strodel, B, Kayed, R, Lesné, S, Wei, G, Sterpone, F, Doig, AJ & Derreumaux, P 2021, 'Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis', Chemical Reviews, vol. 121, no. 4, pp. 2545-2647. https://doi.org/10.1021/acs.chemrev.0c01122
Christy, TW, Giannetti, CA, Houlihan, G, Smola, MJ, Rice, GM, Wang, J, Dokholyan, NV, Laederach, A, Holliger, P & Weeks, KM 2021, 'Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP', Biochemistry, vol. 60, no. 25, pp. 1971-1982. https://doi.org/10.1021/acs.biochem.1c00270
Vishweshwaraiah, YL, Chen, J & Dokholyan, NV 2021, 'Engineering an allosteric control of protein function', Journal of Physical Chemistry B, vol. 125, no. 7, pp. 1806-1814. https://doi.org/10.1021/acs.jpcb.0c11640
Fan, M, Wang, J, Jiang, H, Feng, Y, Mahdavi, M, Madduri, K, Kandemir, MT & Dokholyan, NV 2021, 'GPU-Accelerated Flexible Molecular Docking', Journal of Physical Chemistry B, vol. 125, no. 4, pp. 1049-1060. https://doi.org/10.1021/acs.jpcb.0c09051
Muralidharan, A, Samoshkin, A, Convertino, M, Piltonen, MH, Gris, P, Wang, J, Jiang, C, Klares, R, Linton, A, Ji, RR, Maixner, W, Dokholyan, NV, Mogil, JS & Diatchenko, L 2021, 'Identification and characterization of novel candidate compounds targeting 6- and 7-transmembrane μ-opioid receptor isoforms', British Journal of Pharmacology, vol. 178, no. 13, pp. 2709-2726. https://doi.org/10.1111/bph.15463
Khazan, N, Kim, KK, Hansen, JN, Singh, NA, Moore, T, Snyder, CWA, Pandita, R, Strawderman, M, Fujihara, M, Takamura, Y, Jian, Y, Battaglia, N, Yano, N, Teramoto, Y, Arnold, LA, Hopson, R, Kishor, K, Nayak, S, Ojha, D, Sharon, A, Ashton, JM, Wang, J, Milano, MT, Miyamoto, H, Linehan, DC, Gerber, SA, Kawar, N, Singh, AP, Tabdanov, ED, Dokholyan, NV, Kakuta, H, Jurutka, PW, Schor, NF, Rowswell-Turner, RB, Singh, RK & Moore, RG 2022, 'Identification of a Vitamin-D Receptor Antagonist, MeTC7, which Inhibits the Growth of Xenograft and Transgenic Tumors in Vivo', Journal of Medicinal Chemistry, vol. 65, no. 8, pp. 6039-6055. https://doi.org/10.1021/acs.jmedchem.1c01878
Li, J, Alam, M, Sha, CM, Wang, J, Dokholyan, NV & Ghosh, S 2021, Invited: Drug Discovery Approaches using Quantum Machine Learning. in 2021 58th ACM/IEEE Design Automation Conference, DAC 2021. Proceedings - Design Automation Conference, vol. 2021-December, Institute of Electrical and Electronics Engineers Inc., pp. 1356-1359, 58th ACM/IEEE Design Automation Conference, DAC 2021, San Francisco, United States, 12/5/21. https://doi.org/10.1109/DAC18074.2021.9586268
Chirasani, VR, Popov, KI, Meissner, G & Dokholyan, NV 2022, 'Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1', Proteins: Structure, Function and Bioinformatics, vol. 90, no. 2, pp. 385-394. https://doi.org/10.1002/prot.26228
Zhovmer, AS, Manning, A, Smith, C, Hayes, JB, Burnette, DT, Wang, J, Cartagena-Rivera, AX, Dokholyan, NV, Singh, RK & Tabdanov, ED 2021, 'Mechanical Counterbalance of Kinesin and Dynein Motors in a Microtubular Network Regulates Cell Mechanics, 3D Architecture, and Mechanosensing', ACS nano, vol. 15, no. 11, pp. 17528-17548. https://doi.org/10.1021/acsnano.1c04435
Landoni, E, Fuca, G, Wang, J, Chirasani, VR, Yao, Z, Dukhovlinova, E, Ferrone, S, Savoldo, B, Hong, LK, Shou, P, Musio, S, Padelli, F, Finocchiaro, G, Droste, M, Kuhlman, B, Shamshiev, A, Pellegatta, S, Dokholyan, NV & Dotti, G 2021, 'Modifications to the framework regions eliminate chimeric antigen receptor tonic signaling', Cancer Immunology Research, vol. 9, no. 4, pp. 441-453. https://doi.org/10.1158/2326-6066.CIR-20-0451
Dokholyan, NV 2021, 'Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming', NPJ systems biology and applications, vol. 7, no. 1, 15. https://doi.org/10.1038/s41540-021-00176-8
Choi, ES & Dokholyan, NV 2021, 'SOD1 oligomers in amyotrophic lateral sclerosis', Current Opinion in Structural Biology, vol. 66, pp. 225-230. https://doi.org/10.1016/j.sbi.2020.12.002
Vann, KR, Vishweshwaraiah, YL, Dokholyan, NV & Kutateladze, TG 2021, 'Searching for methyllysine-binding aromatic cages', Biochemical Journal, vol. 478, no. 19, pp. 3613-3619. https://doi.org/10.1042/BCJ20210106
Serpa, JJ, Popov, KI, Petrotchenko, EV, Dokholyan, NV & Borchers, CH 2021, 'Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations', Proteomics, vol. 21, no. 21-22, 2000298. https://doi.org/10.1002/pmic.202000298
Chen, J, Zaer, S, Drori, P, Zamel, J, Joron, K, Kalisman, N, Lerner, E & Dokholyan, NV 2021, 'The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds', Structure, vol. 29, no. 9, pp. 1048-1064.e6. https://doi.org/10.1016/j.str.2021.05.002
Reilley, DJ, Wang, J, Dokholyan, NV & Alexandrova, AN 2021, 'Titr-DMD - A rapid, coarse-grained Quasi-All-Atom constant pH molecular dynamics framework', Journal of Chemical Theory and Computation, vol. 17, no. 7, pp. 4538-4549. https://doi.org/10.1021/acs.jctc.1c00338
Vishweshwaraiah, YL, Chen, J, Chirasani, VR, Tabdanov, ED & Dokholyan, NV 2021, 'Two-input protein logic gate for computation in living cells', Nature communications, vol. 12, no. 1, 6615. https://doi.org/10.1038/s41467-021-26937-x

2020

Tyagi, A, Chandrasekaran, B, Kolluru, V, Baby, BV, Sripathi, CA, Ankem, MK, Ramisetti, SR, Chirasani, VR, Dokholyan, NV, Sharma, AK & Damodaran, C 2020, 'ASR490, a small molecule, overrides aberrant expression of notch1 in colorectal cancer', Molecular cancer therapeutics, vol. 19, no. 12, pp. 2422-2431. https://doi.org/10.1158/1535-7163.MCT-19-0949
Piltonen, M, Krokhotin, A, Parisien, M, Bérubé, P, Djambazian, H, Sladek, R, Dokholyan, NV, Shabalina, SA & Diatchenko, L 2021, 'Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants', Cellular and Molecular Neurobiology, vol. 41, no. 5, pp. 1039-1055. https://doi.org/10.1007/s10571-020-00971-7
Piltonen, M, Krokhotin, A, Parisien, M, Bérubé, P, Djambazian, H, Sladek, R, Dokholyan, NV, Shabalina, SA & Diatchenko, L 2021, 'Correction to: Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants (Cellular and Molecular Neurobiology, (2021), 41, 5, (1039-1055), 10.1007/s10571-020-00971-7)', Cellular and Molecular Neurobiology, vol. 41, no. 5, pp. 1057. https://doi.org/10.1007/s10571-020-00999-9
Dinavahi, SS, Gowda, R, Gowda, K, Bazewicz, CG, Chirasani, VR, Battu, MB, Berg, A, Dokholyan, NV, Amin, S & Robertson, GP 2020, 'Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent', Molecular cancer therapeutics, vol. 19, no. 2, pp. 447-459. https://doi.org/10.1158/1535-7163.MCT-19-0360
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Jiang, H, Fan, M, Wang, J, Sarma, A, Mohanty, S, Dokholyan, NV, Mahdavi, M & Kandemir, MT 2020, 'Guiding conventional protein-ligand docking software with convolutional neural networks', Journal of Chemical Information and Modeling, vol. 60, no. 10, pp. 4594-4602. https://doi.org/10.1021/acs.jcim.0c00542
Makepeace, KAT, Brodie, NI, Popov, KI, Gudavicius, G, Nelson, CJ, Petrotchenko, EV, Dokholyan, NV & Borchers, CH 2020, 'Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations', Journal of Proteomics, vol. 211, 103544. https://doi.org/10.1016/j.jprot.2019.103544
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Miao, Z, Adamiak, RW, Antczak, M, Boniecki, MJ, Bujnicki, J, Chen, SJ, Cheng, CY, Cheng, Y, Chou, FC, Das, R, Dokholyan, NV, Ding, F, Geniesse, C, Jiang, Y, Joshi, A, Krokhotin, A, Magnus, M, Mailhot, O, Major, F, Mann, TH, Piątkowski, P, Pluta, R, Popenda, M, Sarzynska, J, Sun, L, Szachniuk, M, Tian, S, Wang, J, Wang, J, Watkins, AM, Wiedemann, J, Xiao, Y, Xu, X, Yesselman, JD, Zhang, D, Zhang, Y, Zhang, Z, Zhao, C, Zhao, P, Zhou, Y, Zok, T, Żyła, A, Ren, A, Batey, RT, Golden, BL, Huang, L, Lilley, DM, Liu, Y, Patel, DJ & Westhof, E 2020, 'RNA-Puzzles round IV: 3D Structure predictions of four ribozymes and two aptamers', RNA, vol. 26, no. 8, pp. 982-995. https://doi.org/10.1261/RNA.075341.120
Wu, HD, Kikuchi, M, Dagliyan, O, Aragaki, AK, Nakamura, H, Dokholyan, NV, Umehara, T & Inoue, T 2020, 'Rational design and implementation of a chemically inducible heterotrimerization system', Nature methods, vol. 17, no. 9, pp. 928-936. https://doi.org/10.1038/s41592-020-0913-x
Xu, L, Harms, FL, Chirasani, VR, Pasek, DA, Kortüm, F, Meinecke, P, Dokholyan, NV, Kutsche, K & Meissner, G 2020, 'Single-channel properties of skeletal muscle ryanodine receptor pore Δ4923FF4924 in two brothers with a lethal form of fetal akinesia', Cell Calcium, vol. 87, 102182. https://doi.org/10.1016/j.ceca.2020.102182
Ono, C, Fukuhara, T, Li, S, Wang, J, Sato, A, Izumi, T, Fauzyah, Y, Yamamoto, T, Morioka, Y, Dokholyan, NV, Standley, DM & Matsuura, Y 2020, 'Various miRNAs compensate the role of miR-122 on HCV replication', PLoS pathogens, vol. 16, no. 6 June, e1008308. https://doi.org/10.1371/journal.ppat.1008308
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