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 Models Ligands Amino Acids Opioid Receptors Biological Systems Genes Rna Computational Biology Molecular Dynamics Therapeutics Phenotype Genetic Engineering Biophysics Alternative Splicing Protein Folding Engineering Graphics Processing Unit Nucleic Acid Conformation Mutagenesis Amyloid Molecules Mutant Proteins Synthetic Biology G Protein Coupled Receptors

Most Recent Papers

Nanoscale programming of cellular and physiological phenotypes

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

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

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

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

Activating Sphingosine-1-phospahte signaling in endothelial cells increases myosin light chain phosphorylation to decrease endothelial permeability thereby inhibiting cancer metastasis

Yu Chi Chen, Saketh S. Dinavahi, Qilong Feng, Raghavendra Gowda, Srinivasa Ramisetti, Xinghai Xia, Kyle B. LaPenna, Venkat R. Chirasani, Sung Hyun Cho, Susan L. Hafenstein, Madhu Babu Battu, Arthur Berg, Arun K. Sharma, Tom Kirchhausen, Nikolay V. Dokholyan, Shantu Amin, Pingnian He, Gavin P. Robertson, 2021, Cancer Letters on p. 107-119

Modifications to the framework regions eliminate chimeric antigen receptor tonic signaling

Elisa Landoni, Giovanni Fuca, Jian Wang, Venkat R. Chirasani, Zhiyuan Yao, Elena Dukhovlinova, Soldano Ferrone, Barbara Savoldo, Lee K. Hong, Peishun Shou, Silvia Musio, Francesco Padelli, Gaetano Finocchiaro, Miriam Droste, Brian Kuhlman, Abdijapar Shamshiev, Serena Pellegatta, Nikolay V. Dokholyan, Gianpietro Dotti, 2021, Cancer immunology research on p. 441-453

Prefusion spike protein stabilization through computational mutagenesis

Dong Yan Zhang, Jian Wang, Nikolay V. Dokholyan, 2021, Proteins: Structure, Function and Genetics on p. 399-408

Engineering an allosteric control of protein function

Yashavantha L. Vishweshwaraiah, Jiaxing Chen, Nikolay V. Dokholyan, 2021, Journal of Physical Chemistry B on p. 1806-1814

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

GPU-Accelerated Flexible Molecular Docking

Mengran Fan, Jian Wang, Huaipan Jiang, Yilin Feng, Mehrdad Mahdavi, Kamesh Madduri, Mahmut T. Kandemir, Nikolay V. Dokholyan, 2021, Journal of Physical Chemistry B on p. 1049-1060

Most-Cited Papers

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

Irina Kufareva, Manuel Rueda, Vsevolod Katritch, Raymond C. Stevens, Ruben Abagyan, Yasushi Yoshikawa, Toshio Furuya, Huisun Lee, Ambrish Roy, John Grime, Joseph Rebehmed, Yang Zhang, Luc Roumen, Iwan J.P. de Esch, Rob Leurs, Chris de Graaf, Youyong Li, Tingjun Hou, Michael M. Mysinger, Dahlia R. Weiss, John J. Irwin, Brian K. Shoichet, Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers, Elizabeth Yuriev, Qi Wang, Robert H. Mach, David E. Reichert, Gwo Yu Chuang, Didier Rognan, John Simms, Patrick Sexton, Denise Wootten, Dorota Latek, Umesh Ghoshdastider, Slawomir Filipek, LenServer, Andrea Kirkpatrick, Bartosz Trzaskowski, Adam Griffith, Soo Kyung Kim, Ravinder Abrol, William A. Goddard, Nagarajan Vaidehi, Alfonso Lam, Supriyo Bhattacharya, Hubert Li, Gouthaman Balaraman, Michiel Niesen, Sandeep Pal, Victor Solovyev, Yrii Vorobjev, Natalia Bakulina, Thijs Beuming, Stefano Costanzi, Lei Shi, Chris Higgs, Noeris Salam, Dmitry Lupyan, Woody Sherman, Feng Ding, Pradeep Kota, Srinivas Ramachandran, Nikolay V. Dokholyan, Jens Carlsson, Ryan G. Coleman, Hao Fan, Avner Schlessinger, John J. Irwin, Andrej Sali, Brian K. Shoichet, Irina Tikhonova, Irina Pogozheva, Andrei Lomize, Nathan E. Hall, Muhammad Muddassa, Yang Zhang, Ae Nim Pae, Jooyoung Lee, Laura Lopez, Cristian Obiol-Pardo, Jana Selent, Sadia Mahboob, Tim Werner, W. Bret Church, Michal Brylinski, Tadashi Ando, Aysam Guerler, Hongyi Zhou, Jeffrey Skolnick, Henri Xhaard, Wiktor Jurkowski, Arne Elofsson, Ahsan K. Murad, Malgorzata Drwal, Tom B. Dupree, Renate Griffith, Liliana Ostopovici-Halip, Cristian Bologa, K. M. Chen, J. Sun, Patrick Barth, Vladimir Yarov-Yarovoy, David Baker, Bas Vroling, Marijn P.A. Sanders, Sander B. Nabuurs, Gregory V. Nikiforovich, 2011, Structure with Folding & design on p. 1108-1126

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

Automated minimization of steric clashes in protein structures

Srinivas Ramachandran, Pradeep Kota, Feng Ding, Nikolay V. Dokholyan, 2011, Proteins: Structure, Function and Genetics on p. 261-270

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

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

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

Controlling Allosteric Networks in Proteins

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