Nikolay Dokholyan

Nikolay Dokholyan

G. Thomas Passananti Professor

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Bio

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

Publication Tags

Proteins Molecular Models Phosphorylation Antibodies Molecular Dynamics Simulation Ligands Amino Acids Mutation Molecular Dynamics Carbohydrates Dimerization Chemical Activation Mutagenesis Proteomics Enzymes Rna Therapeutics Nucleic Acid Conformation Morphine Computational Biology Computer Simulation Binding Sites Cystic Fibrosis Transmembrane Conductance Regulator Thymidylate Synthase Opioid Receptors

Most Recent Papers

Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations

Karl A.T. Makepeace, Nicholas I. Brodie, Konstantin I. Popov, Geoff Gudavicius, Christopher J. Nelson, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers, 2020, Journal of Proteomics

Computationally Guided Design of Single-Chain Variable Fragment Improves Specificity of Chimeric Antigen Receptors

Andrey Krokhotin, Hongwei Du, Koichi Hirabayashi, Konstantin Popov, Tomohiro Kurokawa, Xinhui Wan, Soldano Ferrone, Gianpietro Dotti, Nikolay V. Dokholyan, 2019, Molecular Therapy - Oncolytics on p. 30-37

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

Cheng Zhu, Elena Dukhovlinova, Olivia Council, Lihua Ping, Edgar M. Faison, Shamit S. Prabhu, E. Lake Potter, Stephen L. Upton, Guowei Yin, James M. Fay, Laura P. Kincer, Ean Spielvogel, Sharon L. Campbell, S. Rahima Benhabbour, Hengming Ke, Ronald Swanstrom, Nikolay V. Dokholyan, 2019, Nature communications

MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression

Yao Jiang, Yanqiong Zhang, Janet Y. Leung, Cheng Fan, Konstantin I. Popov, Siyuan Su, Jiayi Qian, Xiaodong Wang, Alisha Holtzhausen, Eric Ubil, Yang Xiang, Ian Davis, Nikolay V. Dokholyan, Gang Wu, Charles M. Perou, William Y. Kim, H. Shelton Earp, Pengda Liu, 2019, Nature communications

Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins

Silvia Bonfanti, Maria Chiara Lionetti, Maria Rita Fumagalli, Venkat R. Chirasani, Guido Tiana, Nikolay V. Dokholyan, Stefano Zapperi, Caterina A.M. La Porta, 2019, Scientific reports

Insight into the Structure of the “Unstructured” Tau Protein

Konstantin I. Popov, Karl A.T. Makepeace, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers, 2019, Structure on p. 1710-1715.e4

Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences

Andrey Krokhotin, Muzaddid Sarker, Ernesto Alva Sevilla, Lindsey M. Costantini, Jack D. Griffith, Sharon L. Campbell, Nikolay V. Dokholyan, 2019, Structure on p. 1527-1536.e3

Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling

Cheng Zhu, Qingjian Han, Alexander Samoshkin, Marino Convertino, Alexander Linton, Edgar M. Faison, Ru Rong Ji, Luda Diatchenko, Nikolay V. Dokholyan, 2019, Proteins: Structure, Function and Bioinformatics on p. 878-884

A central core disease mutation in the Ca<sup>2+</sup>-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation

Venkat R. Chirasani, Le Xu, Hannah G. Addis, Daniel A. Pasek, Nikolay V. Dokholyan, Gerhard Meissner, Naohiro Yamaguchi, 2019, American Journal of Physiology - Cell Physiology on p. C358-C365

Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase

Paul J. Sapienza, Konstantin I. Popov, David D. Mowrey, Bradley T. Falk, Nikolay Dokholyan, Andrew L. Lee, 2019, Biochemistry on p. 3302-3313

Recent 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 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 Bioinformatics on p. 261-270

Engineered allosteric activation of kinases in living cells

Andrei V. Karginov, Feng Ding, Pradeep Kota, Nikolay V. Dokholyan, Klaus M. Hahn, 2010, Nature Biotechnology on p. 743-747

Discrete molecular dynamics

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

Correctors of δF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

Lihua He, Pradeep Kota, Andrei A. Aleksandrov, Liying Cui, Tim Jensen, Nikolay V. Dokholyan, John R. Riordan, 2013, FASEB Journal on p. 536-545

Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP

Andrei V. Karginov, Yan Zou, David Shirvanyants, Pradeep Kota, Nikolay V. Dokholyan, Douglas D. Young, Klaus M. Hahn, Alexander Deiters, 2011, Journal of the American Chemical Society on p. 420-423

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 (New York, N.Y.) 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