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 Molecular Dynamics Protein Molecular Models Rna Opioid Receptors Ligands Biological Systems Simulation Atoms Genes Sampling Amino Acids Therapeutics Alternative Splicing Computational Biology Phenotype Genetic Engineering Protein Folding Biophysics Nucleic Acid Conformation Synthetic Biology Molecule Protein Structure Allosteric Regulation

Most Recent Papers

Invited

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

Nanoscale programming of cellular and physiological phenotypes

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

Two-input protein logic gate for computation in living cells

Yashavantha L. Vishweshwaraiah, Jiaxing Chen, Venkat R. Chirasani, Erdem D. Tabdanov, Nikolay V. Dokholyan, 2021, Nature Communications

Mechanical Counterbalance of Kinesin and Dynein Motors in a Microtubular Network Regulates Cell Mechanics, 3D Architecture, and Mechanosensing

Alexander S. Zhovmer, Alexis Manning, Chynna Smith, James B. Hayes, Dylan T. Burnette, Jian Wang, Alexander X. Cartagena-Rivera, Nikolay V. Dokholyan, Rakesh K. Singh, Erdem D. Tabdanov, 2021, ACS Nano on p. 17528-17548

Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

Jason J. Serpa, Konstantin I. Popov, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers, 2021, Proteomics

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Jiaxing Chen, Sofia Zaer, Paz Drori, Joanna Zamel, Khalil Joron, Nir Kalisman, Eitan Lerner, Nikolay V. Dokholyan, 2021, Structure with Folding & design on p. 1048-1064.e6

Titr-DMD - A rapid, coarse-grained Quasi-All-Atom constant pH molecular dynamics framework

David J. Reilley, Jian Wang, Nikolay V. Dokholyan, Anastassia N. Alexandrova, 2021, Journal of Chemical Theory and Computation on p. 4538-4549

Correction to

Marjo Piltonen, Andrey Krokhotin, Marc Parisien, Pierre Bérubé, Haig Djambazian, Rob Sladek, Nikolay V. Dokholyan, Svetlana A. Shabalina, Luda Diatchenko, 2021, Cellular and Molecular Neurobiology on p. 1057

Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants

Marjo Piltonen, Andrey Krokhotin, Marc Parisien, Pierre Bérubé, Haig Djambazian, Rob Sladek, Nikolay V. Dokholyan, Svetlana A. Shabalina, Luda Diatchenko, 2021, Cellular and Molecular Neurobiology on p. 1039-1055

Identification and characterization of novel candidate compounds targeting 6- and 7-transmembrane μ-opioid receptor isoforms

Arjun Muralidharan, Alexander Samoshkin, Marino Convertino, Marjo Hannele Piltonen, Pavel Gris, Jian Wang, Changyu Jiang, Richard Klares, Alexander Linton, Ru Rong Ji, William Maixner, Nikolay V. Dokholyan, Jeffrey S. Mogil, Luda Diatchenko, 2021, British Journal of Pharmacology on p. 2709-2726

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

Discrete molecular dynamics

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

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

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

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

Controlling Allosteric Networks in Proteins

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

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

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 III

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

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).