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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

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

Recent Publications


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.
Sha, CM, Wang, J & Dokholyan, NV 2024, 'Differentiable rotamer sampling with molecular force fields', Briefings in bioinformatics, vol. 25, no. 1, slad183.
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.
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.
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.


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.
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.
Godbole, SS & Dokholyan, NV 2023, 'Allosteric regulation of kinase activity in living cells', eLife, vol. 12, RP90574.
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.
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.
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.
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.
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.
Afonin, KA & Dokholyan, NV 2023, 'Editorial to “Molecular engineering of biomaterials programmed to operate in living systems”', Advanced Drug Delivery Reviews, vol. 193, 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.
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.
Sha, CM, Wang, J & Dokholyan, NV 2023, 'Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks', Biophysical journal.
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.
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.
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.
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.


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.
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.
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.
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.
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.
Chen, J, Vishweshwaraiah, YL & Dokholyan, NV 2022, 'Design and engineering of allosteric communications in proteins', Current Opinion in Structural Biology, vol. 73, 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.
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.
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.
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.
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.
Sha, CM, Wang, J & Dokholyan, NV 2022, 'NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules', Frontiers in Molecular Biosciences, vol. 9, 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.
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.
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.
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.
Vishweshwaraiah, YL & Dokholyan, NV 2022, 'Toward rational vaccine engineering', Advanced Drug Delivery Reviews, vol. 183, 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.
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.
Vishweshwaraiah, YL & Dokholyan, NV 2022, 'mRNA vaccines for cancer immunotherapy', Frontiers in immunology, vol. 13, 1029069.


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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Dokholyan, NV 2021, 'Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming', NPJ systems biology and applications, vol. 7, no. 1, 15.
Choi, ES & Dokholyan, NV 2021, 'SOD1 oligomers in amyotrophic lateral sclerosis', Current Opinion in Structural Biology, vol. 66, pp. 225-230.
Vann, KR, Vishweshwaraiah, YL, Dokholyan, NV & Kutateladze, TG 2021, 'Searching for methyllysine-binding aromatic cages', Biochemical Journal, vol. 478, no. 19, pp. 3613-3619.
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.
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.
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.
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.


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.
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.
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.
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.
Dokholyan, NV 2020, 'Experimentally-driven protein structure modeling', Journal of Proteomics, vol. 220, 103777.
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.
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.
Wang, J, Jain, A, McDonald, LR, Gambogi, C, Lee, AL & Dokholyan, NV 2020, 'Mapping allosteric communications within individual proteins', Nature communications, vol. 11, no. 1, 3862.
Zhang, DY, Wang, J & Dokholyan, NV 2021, 'Prefusion spike protein stabilization through computational mutagenesis', Proteins: Structure, Function and Bioinformatics, vol. 89, no. 4, pp. 399-408.
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.
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.
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.
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.