Nikolay Dokholyan

G. Thomas Passananti Professor of Pharmacology; Professor of Biochemistry and Molecular Biology

Nikolay Dokholyan

Research Summary

We are a translational systems research group in the Pharmacology at the Penn State College of Medicine. Our laboratory focuses on understanding etiologies of human diseases, such as cystic fibrosis (CF), amyotrophic lateral sclerosis (ALS), and pain conditions, such as hyperalgesia.

Huck Affiliations

Links

Most Recent Publications

RNA-Puzzles Round V: blind predictions of 23 RNA structures

Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa Rebeca H. de Aquino, Nagendar Goud Badepally, Robert T. Batey, Eugene F. Baulin, Pawel Boinski, Michal J. Boniecki, Janusz M. Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K. Dawson, Frank DiMaio, Feng Ding, Anne Catherine Dock-Bregeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R. Ferré-D’Amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, BenoÎt Masquida, S. Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya P.N. Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A. Piccirilli, Smita Priyadarshini Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C. Suddala, Marta Szachniuk, Raphael Townshend, Robert J. Trachman, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof, Zhichao Miao, 2025, Nature Methods on p. 399-411

Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells

Martin Panigaj, Tanaya Basu Roy, Elizabeth Skelly, Morgan R. Chandler, Jian Wang, Srinivasan Ekambaram, Kristin Bircsak, Nikolay V. Dokholyan, Kirill A. Afonin, 2025, ACS Nano on p. 1865-1883

The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives

Srinivasan Ekambaram, Grigor Arakelov, Nikolay V. Dokholyan, 2025, Journal of Molecular Biology

Optogenetically engineered Septin-7 enhances immune cell infiltration of tumor spheroids

Jiaxing Chen, Brianna Hnath, Congzhou M. Sha, Lynne Beidler, Todd D. Schell, Nikolay V. Dokholyan, 2024, Proceedings of the National Academy of Sciences of the United States of America

2'3'-cGAMP interactome identifies 2'3'-cGAMP/ Rab18/FosB signaling in cell migration control independent of innate immunity

Yu Deng, Quentin Hahn, Le Yu, Zhichuan Zhu, Joshua A. Boyer, Jian Wang, Deyu Kong, Leiah M. Carey, Austin J. Hepperla, Jeremy M. Simon, Brenda Temple, Zhigang Zhang, Yanqiong Zhang, Charlene Santos, Jonathan E. Frank, Laura E. Herring, Xiaodong Wang, Nikolay V. Dokholyan, Sharon L. Campbell, Albert S. Baldwin, Blossom Damania, Qi Zhang, Pengda Liu, 2024, Science advances

Unveiling the double-edged sword: SOD1 trimers possess tissue-selective toxicity and bind septin-7 in motor neuron-like cells

Esther Sue Choi, Brianna Hnath, Congzhou Mike Sha, Nikolay V. Dokholyan, 2024, Structure with Folding & design on p. 1776-1792.e5

Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks

Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, 2024, Biophysical Journal on p. 2671-2681

Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology

Yelixza I. Avila, Laura P. Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David Lilley, Robin E. Stanley, Ya Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi Jie Chen, Nikolay V. Dokholyan, Cheemeng Tan, S. Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W. Binzel, Peixuan Guo, Kirill A. Afonin, 2024, ACS Applied Bio Materials on p. 3587-3604

Application of Quantum Tensor Networks for Protein Classification

Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay Dokholyan, Swaroop Ghosh, 2024, on p. 132-137

Systematic review and meta-analysis of dysregulated microRNAs derived from liquid biopsies as biomarkers for amyotrophic lateral sclerosis

Hemerson Casado Gama, Mariana A. Amorós, Mykaella Andrade de Araújo, Congzhou M. Sha, Mirella P.S. Vieira, Rayssa G.D. Torres, Gabriela F. Souza, Janaína A. Junkes, Nikolay V. Dokholyan, Daniel Leite Góes Gitaí, Marcelo Duzzioni, 2024, Non-coding RNA Research on p. 523-535

Most-Cited Papers

Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis

Phuong H. Nguyen, Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Dominguez, Joan Emma Shea, Nikolay V. Dokholyan, Alfonso de Simone, Buyong Ma, Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesné, Guanghong Wei, Fabio Sterpone, Andrew J. Doig, Philippe Derreumaux, 2021, Chemical Reviews on p. 2545-2647

Allostery in Its Many Disguises: From Theory to Applications

Shoshana J. Wodak, Emanuele Paci, Nikolay V. Dokholyan, Igor N. Berezovsky, Amnon Horovitz, Jing Li, Vincent J. Hilser, Ivet Bahar, John Karanicolas, Gerhard Stock, Peter Hamm, Roland H. Stote, Jerome Eberhardt, Yassmine Chebaro, Annick Dejaegere, Marco Cecchini, Jean Pierre Changeux, Peter G. Bolhuis, Jocelyne Vreede, Pietro Faccioli, Simone Orioli, Riccardo Ravasio, Le Yan, Carolina Brito, Matthieu Wyart, Paraskevi Gkeka, Ivan Rivalta, Giulia Palermo, J. Andrew McCammon, Joanna Panecka-Hofman, Rebecca C. Wade, Antonella Di Pizio, Masha Y. Niv, Ruth Nussinov, Chung Jung Tsai, Hyunbum Jang, Dzmitry Padhorny, Dima Kozakov, Tom McLeish, 2019, Structure with Folding & design on p. 566-578

Controlling Allosteric Networks in Proteins

Nikolay V. Dokholyan, 2016, Chemical Reviews on p. 6463-6487

Engineering extrinsic disorder to control protein activity in living cells

Onur Dagliyan, Miroslaw Tarnawski, Pei Hsuan Chu, David Shirvanyants, Ilme Schlichting, Nikolay V. Dokholyan, Klaus M. Hahn, 2016, Science on p. 1441-1444

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

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Robert T. Batey, Alexander J. Becka, Marcin Biesiada, Michał J. Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Clarence Yu Cheng, Fang Chieh Chou, Adrian R. Ferré-D'Amaré, Rhiju Das, Wayne K. Dawson, Feng Ding, Nikolay V. Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E. Łach, François Major, Thomas H. Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J. Patel, Joseph A. Piccirilli, Mariusz Popenda, Katarzyna J. Purzycka, Aiming Ren, Greggory M. Rice, John Santalucia, Joanna Sarzynska, Marta Szachniuk, Arpit Tandon, Jeremiah J. Trausch, Siqi Tian, Jian Wang, Kevin M. Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof, 2017, RNA on p. 655-672

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Zhichao Miao, Ryszard W. Adamiak, Marc Frédérick Blanchet, Michal Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Clarence Cheng, Grzegorz Chojnowski, Fang Chieh Chou, Pablo Cordero, José Almeida Cruz, Adrian R. Ferré-D'Amaré, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Stanislaw Dunin-Horkawicz, Wipapat Kladwang, Andrey Krokhotin, Grzegorz Lach, Marcin Magnus, François Major, Thomas H. Mann, Benoît Masquida, Dorota Matelska, Mélanie Meyer, Alla Peselis, Mariusz Popenda, Katarzyna J. Purzycka, Alexander Serganov, Juliusz Stasiewicz, Marta Szachniuk, Arpit Tandon, Siqi Tian, Jian Wang, Yi Xiao, Xiaojun Xu, Jinwei Zhang, Peinan Zhao, Tomasz Zok, Eric Westhof, 2015, RNA on p. 1066-1084

Mapping allosteric communications within individual proteins

Jian Wang, Abha Jain, Leanna R. McDonald, Craig Gambogi, Andrew L. Lee, Nikolay V. Dokholyan, 2020, Nature Communications

Physicochemical code for quinary protein interactions in Escherichia coli

Xin Mu, Seongil Choi, Lisa Lang, David Mowray, Nikolay V. Dokholyan, Jens Danielsson, Mikael Oliveberg, 2017, Proceedings of the National Academy of Sciences of the United States of America on p. E4556-E4563

RNA-Puzzles round IV: 3D Structure predictions of four ribozymes and two aptamers

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Michał J. Boniecki, Janusz Bujnicki, Shi Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H. Mann, Paweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzynska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M. Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D. Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof, 2020, RNA on p. 982-995

iFoldRNA v2: Folding RNA with constraints

Andrey Krokhotin, Kevin Houlihan, Nikolay V. Dokholyan, 2015, Bioinformatics on p. 2891-2893

News Articles Featuring Nikolay Dokholyan

Oct 31, 2024

Huck researchers reflect on the 2024 Nobel Prize in Chemistry

This month, the Nobel Prize in Chemistry was awarded to three scientists credited with historic breakthroughs surrounding proteins and their structures. Three Huck researchers working on similar challenges chime in with their thoughts.

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Oct 23, 2024

Re-engineered, blue light-activated immune cells penetrate and kill solid tumors

A team led by researchers from the Penn State College of Medicine has re-engineered immune cells so that they can penetrate and kill solid tumors grown in the lab.

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Oct 11, 2024

Toxic protein may contribute to ALS development

New study elucidates the physiological processes that may contribute to ALS development and identifies a potential therapeutic target

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Jul 31, 2023

Penn State CTSI announces seven Bridges to Translation pilot funding recipients

Penn State Clinical and Translational Science Institute is helping to generate innovative health research ideas and promote collaboration through the awarding of pilot grants in its "Bridges to Translation" program.

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May 26, 2023

Protein-based nano-‘computer’ evolves in ability to influence cell behavior

The first protein-based nano-computing agent that functions as a circuit has been created by Penn State researchers.

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Oct 26, 2022

Penn State researchers to explore using quantum computers to design new drugs

The time it takes medicines to move from discovery to approved use for patients can take decades and cost billions of dollars. Now, a $1.2 million National Science Foundation grant will help a team of Penn State researchers study the use of quantum computer-based artificial intelligence (AI) to see if quantum computers can bring drugs to patients faster and cheaper.

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Oct 25, 2022

Penn State scientists developing mutation-proof COVID vaccine

Each year, doctors urge people to get a flu shot because the virus changes and requires a new vaccine. A similar pattern seems to be appearing for COVID every time a new variant is discovered.

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Oct 19, 2022

Penn State researchers engineer protein that could be used to develop 1-dose covid vaccine

Despite receiving one of the three covid-19 vaccines available in the U.S., many Americans continue to become infected with the virus.

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Oct 18, 2022

Newly engineered protein could be used to develop adaptation-proof COVID vaccine

A vaccine design approach that could protect against new variants of SARS-CoV-2 — the virus that causes COVID-19 — but also potentially protects against other coronaviruses is one step closer to reality as a result of research at Penn State College of Medicine.

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Nov 16, 2021

Nanoscale ‘computer’ controls function of protein, influences cell behavior

The creation of nanoscale computers for use in precision health care has long been a dream of many scientists and health care providers. Now, for the first time, researchers at Penn State have produced a nanocomputing agent that can control the function of a particular protein that is involved in cell movement and cancer metastasis.

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Mar 26, 2020

Researchers mobilize to study COVID-19 from multiple angles

Penn State funds 17 research proposals, ranging from vaccine development to improved predictive modeling, with more to come.

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Mar 23, 2020

Penn State funds first round of COVID-19 research proposals

One week after launching a rapid-fire call for proposals, awards are granted to six projects that address the global pandemic, with more to follow

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Nov 26, 2019

Fourteen Penn State faculty recognized with lifetime honor

Fourteen Penn State faculty members in areas ranging from physics and engineering to entomology and plant science have been named fellows of the American Association for the Advancement of Science (AAAS), the world’s largest general scientific society. A lifetime honor bestowed upon members by their peers, a total of 443 individuals are being recognized for their extraordinary achievements in advancing science.

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Sep 17, 2019

Research suggests how environmental toxin produced by algae may lead to ALS

Can a computer be used to explain why an environmental toxin might lead to neurodegenerative disease? According to Penn State College of Medicine researchers, a computer generated-simulation allowed them to see how a toxin produced by algal blooms in saltwater might cause Amyotrophic Lateral Sclerosis (ALS).

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