Nikolay V Dokholyan

ResearcherID Scopus Author ID Scopus Author ID ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 92

Top Venues

Nature communications

Briefings in bioinformatics

ACS applied bio materials

bioRxiv : the preprint server for biology

Penn State College of Medicine

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Penn State College of Medicine Jul 16 2018

United States

G. Thomas Passananti Professor, Vice Chair for Research :: Pharmacology

University of North Carolina at Chapel Hill School of Medicine Sep 01 2002 - Jul 15 2018

United States

Professor :: Biochemistry & Biophysics

Publications

Laura P Rebolledo, Weina Ke, Edward Cedrone, Jian Wang, Krishna Majithia, M Brittany Johnson, Nikolay V Dokholyan, Marina A Dobrovolskaia, Kirill A Afonin
Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS applied materials & interfaces 16 (7) (2024)
Dong Yan Zhang, Jian Wang, Gangtong Huang, Sara Langberg, Feng Ding, Nikolay V Dokholyan
APOE regulates the transport of GM1. bioRxiv : the preprint server for biology (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials 7 (6) (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials (2024)
Yashavantha L Vishweshwaraiah, Brianna Hnath, Jian Wang, Morgan Chandler, Arnab Mukherjee, Neela H Yennawar, Squire J Booker, Kirill A Afonin, Nikolay V Dokholyan
A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2. ACS applied bio materials 7 (5) (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials 7 (6) (2024)
Yashavantha L Vishweshwaraiah, Brianna Hnath, Jian Wang, Morgan Chandler, Arnab Mukherjee, Neela H Yennawar, Squire J Booker, Kirill A Afonin, Nikolay V Dokholyan
A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2. ACS applied bio materials (2024)
Yashavantha L Vishweshwaraiah, Brianna Hnath, Jian Wang, Morgan Chandler, Arnab Mukherjee, Neela H Yennawar, Squire J Booker, Kirill A Afonin, Nikolay V Dokholyan
A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2. ACS applied bio materials 7 (5) (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials 7 (6) (2024)
Laura P Rebolledo, Weina Ke, Edward Cedrone, Jian Wang, Krishna Majithia, M Brittany Johnson, Nikolay V Dokholyan, Marina A Dobrovolskaia, Kirill A Afonin
Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS applied materials & interfaces 16 (7) (2024)
Laura P Rebolledo, Weina Ke, Edward Cedrone, Jian Wang, Krishna Majithia, M Brittany Johnson, Nikolay V Dokholyan, Marina A Dobrovolskaia, Kirill A Afonin
Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS applied materials & interfaces 16 (7) (2024)
Yashavantha L Vishweshwaraiah, Brianna Hnath, Jian Wang, Morgan Chandler, Arnab Mukherjee, Neela H Yennawar, Squire J Booker, Kirill A Afonin, Nikolay V Dokholyan
A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2. ACS applied bio materials 7 (5) (2024)
Laura P Rebolledo, Weina Ke, Edward Cedrone, Jian Wang, Krishna Majithia, M Brittany Johnson, Nikolay V Dokholyan, Marina A Dobrovolskaia, Kirill A Afonin
Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS applied materials & interfaces (2024)
Hannah Johnson, Amandeep Singh, Asif Raza, Congzhou M Sha, Jian Wang, Krishne Gowda, Zhihang Shen, Haritha Nair, Chenglong Li, Nikolay V Dokholyan, Satya Narayan, Arun K Sharma
Identification of a Novel Protein Phosphatase 2A Activator, PPA24, as a Potential Therapeutic for FOLFOX-Resistant Colorectal Cancer. Journal of medicinal chemistry (2024)
Laura P Rebolledo, Weina Ke, Edward Cedrone, Jian Wang, Krishna Majithia, M Brittany Johnson, Nikolay V Dokholyan, Marina A Dobrovolskaia, Kirill A Afonin
Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS applied materials & interfaces 16 (7) (2024)
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
Vitamin D Receptor Antagonist MeTC7 Inhibits PD-L1. Cancers 15 (13) (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Jiaxing Chen, Yashavantha L Vishweshwaraiah, Richard B Mailman, Erdem D Tabdanov, Nikolay V Dokholyan
A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments. Science advances 9 (21) (2023)
Shivani Godbole, Nikolay V Dokholyan
Allosteric regulation of kinase activity in living cells. bioRxiv : the preprint server for biology (2023)
Wesley M Raup-Konsavage, Diana E Sepulveda, Jian Wang, Nikolay V Dokholyan, Kent E Vrana, Nicholas M Graziane
Antinociceptive Effects of Cannabichromene (CBC) in Mice: Insights from von Frey, Tail-Flick, Formalin, and Acetone Tests. Biomedicines 12 (1) (2023)
Alexander S Zhovmer, Alexis Manning, Chynna Smith, Jian Wang, Xuefei Ma, Denis Tsygankov, Nikolay V Dokholyan, Alexander X Cartagena-Rivera, Rakesh K Singh, Erdem D Tabdanov
Septins Enable T Cell Contact Guidance via Amoeboid-Mesenchymal Switch. bioRxiv : the preprint server for biology (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Abha Jain, Nikolay V Dokholyan, Andrew L Lee
Allosteric inactivation of an engineered optogenetic GTPase. Proceedings of the National Academy of Sciences of the United States of America 120 (14) (2023)
Venkata R Chirasani, Mohammad Ashhar I Khan, Juilee N Malavade, Nikolay V Dokholyan, Brenton D Hoffman, Sharon L Campbell
Molecular basis and cellular functions of vinculin-actin directional catch bonding. Nature communications 14 (1) (2023)
Venkata R Chirasani, Mohammad Ashhar I Khan, Juilee N Malavade, Nikolay V Dokholyan, Brenton D Hoffman, Sharon L Campbell
Molecular basis and cellular functions of vinculin-actin directional catch bonding. Nature communications 14 (1) (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Congzhou M Sha, Jian Wang, Richard B Mailman, Yang Yang, Nikolay V Dokholyan
Quantifying network behavior in the rat prefrontal cortex: a reproducibility crisis. bioRxiv : the preprint server for biology (2023)
Venkata R Chirasani, Mohammad Ashhar I Khan, Juilee N Malavade, Nikolay V Dokholyan, Brenton D Hoffman, Sharon L Campbell
Molecular basis and cellular functions of vinculin-actin directional catch bonding. Nature communications 14 (1) (2023)
Wesley M Raup-Konsavage, Diana E Sepulveda, Jian Wang, Nikolay V Dokholyan, Kent E Vrana, Nicholas M Graziane
Antinociceptive Effects of Cannabichromene (CBC) in Mice: Insights from von Frey, Tail-Flick, Formalin, and Acetone Tests. Biomedicines 12 (1) (2023)
Damian Beasock, Anh Ha, Justin Halman, Martin Panigaj, Jian Wang, Nikolay V Dokholyan, Kirill A Afonin
Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs) via Enzymatic Degradation. Bioconjugate chemistry (2023)
Wesley M Raup-Konsavage, Diana E Sepulveda, Jian Wang, Nikolay V Dokholyan, Kent E Vrana, Nicholas M Graziane
Antinociceptive Effects of Cannabichromene (CBC) in Mice: Insights from von Frey, Tail-Flick, Formalin, and Acetone Tests. Biomedicines 12 (1) (2023)
Shivani Sujay Godbole, Nikolay V Dokholyan
Allosteric regulation of kinase activity in living cells. eLife 12 (2023)
Venkata R Chirasani, Mohammad Ashhar I Khan, Juilee N Malavade, Nikolay V Dokholyan, Brenton D Hoffman, Sharon L Campbell
Molecular basis and cellular functions of vinculin-actin directional catch bonding. Nature communications 14 (1) (2023)
Brianna Hnath, Jiaxing Chen, Joshua Reynolds, Esther Choi, Jian Wang, Dongyan Zhang, Congzhou M Sha, Nikolay V Dokholyan
Big versus small: The impact of aggregate size in disease. Protein science : a publication of the Protein Society (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V Dokholyan, Charles W Carter
Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase. Structural dynamics (Melville, N.Y.) 10 (4) (2023)
Jian Wang, Congzhou M Sha, Nikolay V Dokholyan
Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology. Methods in molecular biology (Clifton, N.J.) 2709 (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Abha Jain, Nikolay V Dokholyan, Andrew L Lee
Allosteric inactivation of an engineered optogenetic GTPase. Proceedings of the National Academy of Sciences of the United States of America 120 (14) (2023)
Venkata R Chirasani, Mohammad Ashhar I Khan, Juilee N Malavade, Nikolay V Dokholyan, Brenton D Hoffman, Sharon L Campbell
Molecular basis and cellular functions of vinculin-actin directional catch bonding. Nature communications 14 (1) (2023)
Congzhou M Sha, Jian Wang, Nikolay V Dokholyan
Differentiable rotamer sampling with molecular force fields. Briefings in bioinformatics 25 (1) (2023)
Mohammad Mahmoudi Gomari, Neda Rostami, Davood Rabiei Faradonbeh, Hamid Reza Asemaneh, Giti Esmailnia, Seyed-Shahryar Arab, Marziye Farsimadan, Arshad Hosseini, Nikolay V Dokholyan
Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation. Proteins 90 (11) (2022)
Dong Yan Zhang, Jian Wang, Rebecca M Fleeman, Madison K Kuhn, Matthew T Swulius, Elizabeth A Proctor, Nikolay V Dokholyan
Monosialotetrahexosylganglioside Promotes Early Aβ42 Oligomer Formation and Maintenance. ACS chemical neuroscience 13 (13) (2022)
Shouhao Zhou, Xinyi Liu, Xinying Fang, Vernon M Chinchilli, Michael Wang, Hong-Gang Wang, Nikolay V Dokholyan, Chan Shen, J Jack Lee
Robust and Efficient Assessment of Potency (REAP) as a quantitative tool for dose-response curve estimation. eLife 11 (2022)
Weina Ke, Morgan Chandler, Edward Cedrone, Renata F Saito, Maria Cristina Rangel, Mara de Souza Junqueira, Jian Wang, Da Shi, Nguyen Truong, Melina Richardson, Lewis A Rolband, Didier Dréau, Peter Bedocs, Roger Chammas, Nikolay V Dokholyan, Marina A Dobrovolskaia, Kirill A Afonin
Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo . Nano letters 22 (14) (2022)
Huaipan Jiang, Jian Wang, Weilin Cong, Yihe Huang, Morteza Ramezani, Anup Sarma, Nikolay V Dokholyan, Mehrdad Mahdavi, Mahmut T Kandemir
Predicting Protein-Ligand Docking Structure with Graph Neural Network. Journal of chemical information and modeling 62 (12) (2022)
Yashavantha L Vishweshwaraiah, Brianna Hnath, Brendan Rackley, Jian Wang, Abhinay Gontu, Morgan Chandler, Kirill A Afonin, Suresh V Kuchipudi, Neil Christensen, Neela H Yennawar, Nikolay V Dokholyan
Adaptation-proof SARS-CoV-2 vaccine design. bioRxiv : the preprint server for biology (2022)
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
Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures. Small (Weinheim an der Bergstrasse, Germany) 18 (13) (2022)
David A Agard, Gregory R Bowman, William F DeGrado, Nikolay V Dokholyan, Huan-Xiang Zhou
Solution of the protein structure prediction problem at last: crucial innovations and next frontiers. Faculty reviews 11 (2022)
David A Agard, Gregory R Bowman, William F DeGrado, Nikolay V Dokholyan, Huan-Xiang Zhou
Solution of the protein structure prediction problem at last: crucial innovations and next frontiers. Faculty reviews 11 (2022)
Mohammad Mahmoudi Gomari, Shadi Abkhiz, Taha Ghantab Pour, Ehsan Lotfi, Neda Rostami, Fatemeh Nafe Monfared, Babak Ghobari, Mona Mosavi, Behruz Alipour, Nikolay V Dokholyan
Peptidomimetics in cancer targeting. Molecular medicine (Cambridge, Mass.) 28 (1) (2022)
Jian Wang, Nikolay V Dokholyan
Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. Journal of chemical information and modeling 62 (3) (2022)
Nikolay V Dokholyan, Richard C Mohs, Randall J Bateman
Challenges and progress in research, diagnostics, and therapeutics in Alzheimer's disease and related dementias. Alzheimer's & dementia (New York, N. Y.) 8 (1) (2022)
Venkata R Chirasani, Konstantin I Popov, Gerhard Meissner, Nikolay V Dokholyan
Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1. Proteins (2021)
Yashavantha L Vishweshwaraiah, Jiaxing Chen, Nikolay V Dokholyan
Engineering an Allosteric Control of Protein Function. The journal of physical chemistry. B 125 (7) (2021)
Jason J Serpa, Konstantin I Popov, Evgeniy V Petrotchenko, Nikolay V Dokholyan, Christoph H Borchers
Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics 21 (21-22) (2021)
Arjun Muralidharan, Alexander Samoshkin, Marino Convertino, Marjo Hannele Piltonen, Pavel Gris, Jian Wang, Changyu Jiang, Richard Klares, Alexander A Linton, Ru-Rong Ji, William Maixner, Nikolay V Dokholyan, Jeffrey S Mogil, Luda Diatchenko
Identification and characterization of novel candidate compounds targeting 6- and 7-transmembrane μ-opioid receptor isoforms. British journal of pharmacology 178 (13) (2021)
David J Reilley, Jian Wang, Nikolay V Dokholyan, Anastassia N Alexandrova
Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework. Journal of chemical theory and computation 17 (7) (2021)
Mengran Fan, Jian Wang, Huaipan Jiang, Yilin Feng, Mehrdad Mahdavi, Kamesh Madduri, Mahmut T Kandemir, Nikolay V Dokholyan
GPU-Accelerated Flexible Molecular Docking. The journal of physical chemistry. B 125 (4) (2021)
Yashavantha L Vishweshwaraiah, Jiaxing Chen, Venkata R Chirasani, Erdem D Tabdanov, Nikolay V Dokholyan
Two-input protein logic gate for computation in living cells. Nature communications 12 (1) (2021)
Phuong Hoang Nguyen, Ayyalusamy Ramamoorthy, Bikash R Sahoo, Jie Zheng, Peter Faller, John E Straub, Laura Domínguez, 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 J McCarty, Mai Suan Li, Carol K 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
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chemical reviews 121 (4) (2021)
Thomas W Christy, Catherine A Giannetti, Gillian Houlihan, Matthew J Smola, Greggory M Rice, Jian Wang, Nikolay V Dokholyan, Alain Laederach, Philipp Holliger, Kevin M Weeks
Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 60 (25) (2021)
Nikolay V Dokholyan
Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming. NPJ systems biology and applications 7 (1) (2021)
Elisa Landoni, Giovanni Fucá, 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
Modifications to the Framework Regions Eliminate Chimeric Antigen Receptor Tonic Signaling. Cancer immunology research 9 (4) (2021)
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
Mechanical Counterbalance of Kinesin and Dynein Motors in a Microtubular Network Regulates Cell Mechanics, 3D Architecture, and Mechanosensing. ACS nano (2021)
Chikako Ono, Takasuke Fukuhara, Songling Li, Jian Wang, Asuka Sato, Takuma Izumi, Yuzy Fauzyah, Takuya Yamamoto, Yuhei Morioka, Nikolay V Dokholyan, Daron M Standley, Yoshiharu Matsuura
Various miRNAs compensate the role of miR-122 on HCV replication. PLoS pathogens 16 (6) (2020)
Dong Yan Zhang, Jian Wang, Nikolay V Dokholyan
Prefusion spike protein stabilization through computational mutagenesis. Proteins 89 (4) (2020)
Zhichiao Miao, Ryszard W Adamiak, Maciej Antczak, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang-Chieh Chou, Rachel J Hagey, Nikolay V Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H Mann, Paweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzyńska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T Batey, Barbara L Golden, Lin Huang, David M J Lilley, Yijin Liu, Dinshaw J Patel, Eric Westhof
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA (New York, N.Y.) 26 (8) (2020)
Huaipan Jiang, Mengran Fan, Jian Wang, Anup Sarma, Shruti Mohanty, Nikolay V Dokholyan, Mehrdad Mahdavi, Mahmut T Kandemir
Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. Journal of chemical information and modeling 60 (10) (2020)
Helen D Wu, Masaki Kikuchi, Onur Dagliyan, Adam K Aragaki, Hideki Nakamura, Nikolay V Dokholyan, Takashi Umehara, Takanari Inoue
Rational design and implementation of a chemically inducible heterotrimerization system. Nature methods 17 (9) (2020)
Jian Wang, Abha Jain, Leanna R McDonald, Craig Gambogi, Andrew L Lee, Nikolay V Dokholyan
Mapping allosteric communications within individual proteins. Nature communications 11 (1) (2020)
Ashish Tyagi, Balaji Chandrasekaran, Venkatesh Kolluru, Becca V Baby, Cibi A Sripathi, Murali K Ankem, Srinivasa R Ramisetti, Venkat R Chirasani, Nikolay V Dokholyan, Arun K Sharma, Chendil Damodaran
ASR490, a Small Molecule, Overrides Aberrant Expression of Notch1 in Colorectal Cancer. Molecular cancer therapeutics 19 (12) (2020)
Onur Dagliyan, Nikolay V Dokholyan, Klaus M Hahn
Engineering proteins for allosteric control by light or ligands. Nature protocols 14 (6) (2019)
Silvia Bonfanti, Maria Chiara Lionetti, Maria Rita Fumagalli, Venkat R Chirasani, Guido Tiana, Nikolay V Dokholyan, Stefano Zapperi, Caterina Anna Maria La Porta
Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins. Scientific reports 9 (1) (2019)
Nicholas I Brodie, Konstantin I Popov, Evgeniy V Petrotchenko, Nikolay V Dokholyan, Christoph H Borchers
Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. PLoS computational biology 15 (3) (2019)
Elizabeth A Proctor, David D Mowrey, Nikolay V Dokholyan
β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology. PLoS computational biology 15 (7) (2019)
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
MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression. Nature communications 10 (1) (2019)
Venkat R Chirasani, Le Xu, Hannah G Addis, Daniel A Pasek, Nikolay V Dokholyan, Gerhard Meissner, Naohiro Yamaguchi
A central core disease mutation in the Ca2+-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation. American journal of physiology. Cell physiology 317 (2) (2019)
Paul J Sapienza, Konstantin I Popov, David D Mowrey, Bradley T Falk, Nikolay V Dokholyan, Andrew L Lee
Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase. Biochemistry 58 (30) (2019)
Saketh S Dinavahi, Raghavendra Gowda, Christopher G Bazewicz, Venkat R Chirasani, Madhu Babu Battu, Arthur Berg, Nikolay V Dokholyan, Shantu Amin, Gavin P Robertson
Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent. Molecular cancer therapeutics 19 (2) (2019)
Jian Wang, Nikolay V Dokholyan
MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. Journal of chemical information and modeling 59 (6) (2019)
David J Reilley, Konstantin I Popov, Nikolay V Dokholyan, Anastassia N Alexandrova
Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding. The journal of physical chemistry. B 123 (21) (2019)
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
Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies. Nature communications 10 (1) (2019)
Cheng Zhu, Qingjian Han, Alexander Samoshkin, Marino Convertino, Alexander A Linton, Edgar M Faison, Ru-Rong Ji, Luda Diatchenko, Nikolay V Dokholyan
Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling. Proteins 87 (10) (2019)
Yuliang Zhang, Mohtadin Hashemi, Zhengjian Lv, Benfeard Williams, Konstantin I Popov, Nikolay V Dokholyan, Yuri L Lyubchenko
High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. The Journal of chemical physics 148 (12) (2018)
Cheng Zhu, Matthew V Beck, Jack D Griffith, Mohanish Deshmukh, Nikolay V Dokholyan
Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences of the United States of America 115 (18) (2018)
Jhuma Das, Andrei A Aleksandrov, Liying Cui, Lihua He, John R Riordan, Nikolay V Dokholyan
Transmembrane helical interactions in the CFTR channel pore. PLoS computational biology 13 (6) (2017)
Xin Mu, Seongil Choi, Lisa Lang, David Mowray, Nikolay V Dokholyan, Jens Danielsson, Mikael Oliveberg
Physicochemical code for quinary protein interactions in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 114 (23) (2017)
Zhichiao 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 Sarzyńska, 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
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA (New York, N.Y.) 23 (5) (2017)
Nicholas I Brodie, Konstantin I Popov, Evgeniy V Petrotchenko, Nikolay V Dokholyan, Christoph H Borchers
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. Science advances 3 (7) (2017)
Mahmoud Shobair, Onur Dagliyan, Pradeep Kota, Yan L Dang, Hong He, M Jackson Stutts, Nikolay V Dokholyan
Gain-of-Function Mutation W493R in the Epithelial Sodium Channel Allosterically Reconfigures Intersubunit Coupling. The Journal of biological chemistry 291 (8) (2015)
Rachel L Redler, Jhuma Das, Juan R Diaz, Nikolay V Dokholyan
Protein Destabilization as a Common Factor in Diverse Inherited Disorders. Journal of molecular evolution 82 (1) (2015)

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Nikolay V Dokholyan