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.

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Publication Tags

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Proteins Protein Therapeutics Mutation Rna Molecular Models Amyotrophic Lateral Sclerosis Computational Biology Vaccines Messenger Rna Nanoparticles Nucleic Acids Escherichia Coli Motor Neurons Hydrogen Fibers Nucleic Acid Conformation Genetic Engineering Thrombin Drug Pharmaceutical Preparations Allosteric Regulation Pharmacology Drug Discovery Signal Transduction

Most Recent Publications

Editorial to “Molecular engineering of biomaterials programmed to operate in living systems”

Kirill A. Afonin, Nikolay V. Dokholyan, 2023, Advanced Drug Delivery Reviews

Structural evolution of Delta lineage of SARS-CoV-2

Mohammad Mahmoudi Gomari, Parastoo Tarighi, Edris Choupani, Shadi Abkhiz, Masoud Mohamadzadeh, Neda Rostami, Esmaeil Sadroddiny, Soukayna Baammi, Vladimir N. Uversky, Nikolay V. Dokholyan, 2023, International Journal of Biological Macromolecules on p. 1116-1140

mRNA vaccines for cancer immunotherapy

Yashavantha L. Vishweshwaraiah, Nikolay V. Dokholyan, 2022, Frontiers in Immunology

Adaptation-Proof SARS-CoV-2 Vaccine Design

Yashavantha L. Vishweshwaraiah, Brianna Hnath, Brendan Rackley, Jian Wang, Abhinay Gontu, Morgan Chandler, Kirill A. Afonin, Suresh V. Kuchipudi, Neil Christensen, Neela H. Yennawar, Nikolay V. Dokholyan, 2022, Advanced Functional Materials

Activation of Disulfide Redox Switch in REDD1 Promotes Oxidative Stress Under Hyperglycemic Conditions

William P. Miller, Congzhou M. Sha, Siddharth Sunilkumar, Allyson L. Toro, Ashley M. Vancleave, Scot R. Kimball, Nikolay V. Dokholyan, Michael D. Dennis, 2022, Diabetes on p. 2764-2776

Peptidomimetics in cancer targeting

Mohammad Mahmoudi Gomari, Shadi Abkhiz, Taha Ghantab Pour, Ehsan Lotfi, Neda Rostami, Fatemeh Nafe Monfared, Babak Ghobari, Mona Mosavi, Behruz Alipour, Nikolay V. Dokholyan, 2022, Molecular Medicine

Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation

Mohammad Mahmoudi Gomari, Neda Rostami, Davood Rabiei Faradonbeh, Hamid Reza Asemaneh, Giti Esmailnia, Shahriar Arab, Marziye Farsimadan, Arshad Hosseini, Nikolay V. Dokholyan, 2022, Proteins: Structure, Function and Genetics on p. 1908-1925

Motor neuron-derived induced pluripotent stem cells as a drug screening platform for amyotrophic lateral sclerosis

Mariana A. Amorós, Esther S. Choi, Axel R. Cofré, Nikolay V. Dokholyan, Marcelo Duzzioni, 2022, Frontiers in Cell and Developmental Biology

Robust and Efficient Assessment of Potency (REAP) as a quantitative tool for dose-response curve estimation

Shouhao Zhou, Xinyi Liu, Xinying Fang, Vernon M. Chinchilli, Michael Wang, Hong Gang Wang, Nikolay V. Dokholyan, Chan Shen, J. Jack Lee, 2022, eLife

Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo

Weina Ke, Morgan Chandler, Edward Cedrone, Renata F. Saito, Maria Cristina Rangel, Mara De Souza Junqueira, Jian Wang, Da Shi, Nguyen Truong, Melina Richardson, Lewis A. Rolband, Didier Dréau, Peter Bedocs, Roger Chammas, Nikolay V. Dokholyan, Marina A. Dobrovolskaia, Kirill A. Afonin, 2022, Nano Letters on p. 5961-5972

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

Cystic fibrosis: Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

Deborah M. Cholon, Nancy L. Quinney, M. Leslie Fulcher, Charles R. Esther, Jhuma Das, Nikolay V. Dokholyan, Scott H. Randell, Richard C. Boucher, Martina Gentzsch, 2014, Science Translational Medicine

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 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

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

Single-molecule correlated chemical probing of RNA

Philip J. Homan, Oleg V. Favorov, Christopher A. Lavender, Olcay Kursun, Xiyuan Ge, Steven Busan, Nikolay V. Dokholyan, Kevin M. Weeks, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 13858-13863

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

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

Elizabeth A. Proctor, Lanette Fee, Yazhong Tao, Rachel L. Redler, James M. Fay, Yuliang Zhang, Zhengjian Lv, Ian P. Mercer, Mohanish Deshmukh, Yuri L. Lyubchenko, Nikolay V. Dokholyan, 2016, Proceedings of the National Academy of Sciences of the United States of America on p. 614-619

News Articles Featuring Nikolay Dokholyan

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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