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 Graduate Students

Huck Affiliations

Links

Publication Tags

Proteins Protein Molecular Models Molecules Biological Systems Rna Amino Acids Ligands Computational Biology Therapeutics Drug Discovery Nucleic Acids Molecular Dynamics Nanoparticles Amyloid Temperature Biophysics Nucleic Acid Conformation Genetic Engineering Phenotype Protein Folding Caffeine Machine Learning Signal Transduction Molecule

Most Recent Papers

AlphaFold illuminates half of the dark human proteins

Jessica L. Binder, Joel Berendzen, Amy O. Stevens, Yi He, Jian Wang, Nikolay V. Dokholyan, Tudor I. Oprea, 2022, Current Opinion in Structural Biology

Multifunctions of α-Synuclein Explained by Its Dynamic Heterogeneous Conformations with a Hierarchy of Transition Times

Jiaxing Chen, Sofia Zaer, Paz Drori, Joanna Zamel, Khalil Joron, Nir Kalisman, Eitan Lerner, Nikolay V. Dokholyan, 2022, FASEB Journal

Design and engineering of allosteric communications in proteins

Jiaxing Chen, Yashavantha L. Vishweshwaraiah, Nikolay V. Dokholyan, 2022, Current Opinion in Structural Biology

Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures

Allison N. Tran, Morgan Chandler, Justin Halman, Damian Beasock, Adam Fessler, Riley Q. McKeough, Phuong Anh Lam, Daniel P. Furr, Jian Wang, Edward Cedrone, Marina A. Dobrovolskaia, Nikolay V. Dokholyan, Susan R. Trammell, Kirill A. Afonin, 2022, Small

Toward rational vaccine engineering

Yashavantha L. Vishweshwaraiah, Nikolay V. Dokholyan, 2022, Advanced Drug Delivery Reviews

NeuralDock

Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, 2022, Frontiers in Molecular Biosciences

Yuel

Jian Wang, Nikolay V. Dokholyan, 2022, Journal of Chemical Information and Modeling on p. 463-471

Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1

Venkat R. Chirasani, Konstantin I. Popov, Gerhard Meissner, Nikolay V. Dokholyan, 2022, Proteins: Structure, Function and Genetics on p. 385-394

Invited

Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh, 2021, on p. 1356-1359

Nanoscale programming of cellular and physiological phenotypes

Nikolay V. Dokholyan, 2021, npj Systems Biology and Applications

Most-Cited Papers

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

RNA-Puzzles

José Almeida Cruz, Marc Frédérick Blanchet, Michal Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Song Cao, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Samuel Coulbourn Flores, Lili Huang, Christopher A. Lavender, Véronique Lisi, François Major, Katarzyna Mikolajczak, Dinshaw J. Patel, Anna Philips, Tomasz Puton, John Santalucia, Fredrick Sijenyi, Thomas Hermann, Kristian Rother, Magdalena Rother, Alexander Serganov, Marcin Skorupski, Tomasz Soltysinski, Parin Sripakdeevong, Irina Tuszynska, Kevin M. Weeks, Christina Waldsich, Michael Wildauer, Neocles B. Leontis, Eric Westhof, 2012, RNA on p. 610-625

Allostery in Its Many Disguises

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

Discrete molecular dynamics

David Shirvanyants, Feng Ding, Douglas Tsao, Srinivas Ramachandran, Nikolay V. Dokholyan, 2012, Journal of Physical Chemistry B on p. 8375-8382

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

Amyloid oligomers

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

The interface of protein structure, protein biophysics, and molecular evolution

David A. Liberles, Sarah A. Teichmann, Ivet Bahar, Ugo Bastolla, Jesse Bloom, Erich Bornberg-Bauer, Lucy J. Colwell, A. P.Jason De Koning, Nikolay V. Dokholyan, Julian Echave, Arne Elofsson, Dietlind L. Gerloff, Richard A. Goldstein, Johan A. Grahnen, Mark T. Holder, Clemens Lakner, Nicholas Lartillot, Simon C. Lovell, Gavin Naylor, Tina Perica, David D. Pollock, Tal Pupko, Lynne Regan, Andrew Roger, Nimrod Rubinstein, Eugene Shakhnovich, Kimmen Sjølander, Shamil Sunyaev, Ashley I. Teufel, Jeffrey L. Thorne, Joseph W. Thornton, Daniel M. Weinreich, Simon Whelan, 2012, Protein Science on p. 769-785

Controlling Allosteric Networks in Proteins

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

The complex molecular biology of Amyotrophic Lateral Sclerosis (ALS)

Rachel L. Redler, Nikolay V. Dokholyan, 2012, Progress in Molecular Biology and Translational Science on p. 215-262

RNA-Puzzles Round II

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

News Articles Featuring Nikolay Dokholyan

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.

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).