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

Publication Tags

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Proteins Protein Molecular Models Rna Escherichia Coli Nucleic Acid Conformation Genetic Engineering Communication Signal Transduction Allosteric Regulation Therapeutics Ligands Src Family Kinases Light Pharmacology Riboswitch Catalytic Rna Allosteric Site Protein Engineering Cystic Fibrosis Cystic Fibrosis Transmembrane Conductance Regulator Amyloid Ivacaftor Catalytic Domain Messenger Rna

Most Recent Publications

Rational peptide design for targeting cancer cell invasion

Mohammad Mahmoudi Gomari, Seyed Shahriar Arab, Saeed Balalaie, Sorour Ramezanpour, Arshad Hosseini, Nikolay V. Dokholyan, Parastoo Tarighi, 2024, Proteins: Structure, Function and Genetics on p. 76-95

Atip Lawanprasert, Janna N. Sloand, Mariangely González Vargas, Harminder Singh, Tomer Eldor, Michael A. Miller, Sopida Pimcharoen, Jian Wang, Scott M. Leighow, Justin R. Pritchard, Nikolay V. Dokholyan, Scott H. Medina, 2023, ChemBioChem

Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V. Dokholyan, Charles W. Carter, 2023, Structural Dynamics

Brianna Hnath, Jiaxing Chen, Joshua Reynolds, Esther Choi, Jian Wang, Dongyan Zhang, Congzhou M. Sha, Nikolay V. Dokholyan, 2023, Protein Science

Negar Khazan, Emily R. Quarato, Niloy A. Singh, Cameron W.A. Snyder, Taylor Moore, John P. Miller, Masato Yasui, Yuki Teramoto, Takuro Goto, Sabeeha Reshi, Jennifer Hong, Naixin Zhang, Diya Pandey, Priyanka Srivastava, Alexandra Morell, Hiroki Kawano, Yuko Kawano, Thomas Conley, Deepak M. Sahasrabudhe, Naohiro Yano, Hiroshi Miyamoto, Omar Aljitawi, Jane Liesveld, Michael W. Becker, Laura M. Calvi, Alexander S. Zhovmer, Erdem D. Tabdanov, Nikolay V. Dokholyan, David C. Linehan, Jeanne N. Hansen, Scott A. Gerber, Ashoke Sharon, Manoj K. Khera, Peter W. Jurutka, Natacha Rochel, Kyu Kwang Kim, Rachael B. Rowswell-Turner, Rakesh K. Singh, Richard G. Moore, 2023, Cancers

Damian Beasock, Anh Ha, Justin Halman, Martin Panigaj, Jian Wang, Nikolay V. Dokholyan, Kirill A. Afonin, 2023, Bioconjugate Chemistry on p. 1139-1146

Jiaxing Chen, Yashavantha L. Vishweshwaraiah, Richard B. Mailman, Erdem D. Tabdanov, Nikolay V. Dokholyan, 2023, Science advances

Structural and dynamic insights into α-synuclein dimer conformations

Joanna Zamel, Jiaxing Chen, Sofia Zaer, Paul David Harris, Paz Drori, Mario Lebendiker, Nir Kalisman, Nikolay V. Dokholyan, Eitan Lerner, 2023, Structure with Folding & design on p. 411-423.e6

Abha Jain, Nikolay V. Dokholyan, Andrew L. Lee, 2023, Proceedings of the National Academy of Sciences of the United States of America

J. A. Reynolds, Y. L. Vishweshwaraiah, V. R. Chirasani, J. R. Pritchard, N. V. Dokholyan, 2023, Journal of Biological Chemistry

Most-Cited Papers

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

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

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

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

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

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

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

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

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

News Articles Featuring Nikolay Dokholyan

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.

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.

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.

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.

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.

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.

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.

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.

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

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.