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ORCIDNikolay V. Dokholyan
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- affiliation: The University of North Carolina at Chapel Hill, Department of Biochemistry and Biophysics, NC, USA
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2020 – today
- 2024
[c2]Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh:
Application of Quantum Tensor Networks for Protein Classification. ACM Great Lakes Symposium on VLSI 2024: 132-137- [i4]Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh:
Application of Quantum Tensor Networks for Protein Classification. CoRR abs/2403.06890 (2024) - 2023
- [i3]Congzhou M. Sha
, Jian Wang, Nikolay V. Dokholyan:
Differentiable Rotamer Sampling with Molecular Force Fields. CoRR abs/2302.11430 (2023) - 2022
- [j29]Jian Wang, Nikolay V. Dokholyan:
Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. J. Chem. Inf. Model. 62(3): 463-471 (2022) - [j28]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. J. Chem. Inf. Model. 62(12): 2923-2932 (2022) - 2021
- [c1]Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh:
Invited: Drug Discovery Approaches using Quantum Machine Learning. DAC 2021: 1356-1359 - [i2]Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh:
Drug Discovery Approaches using Quantum Machine Learning. CoRR abs/2104.00746 (2021) - [i1]Congzhou M. Sha, Nikolay V. Dokholyan:
Simple exponential acceleration of the power iteration algorithm. CoRR abs/2109.10884 (2021) - 2020
- [j27]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. J. Chem. Inf. Model. 60(10): 4594-4602 (2020)
2010 – 2019
- 2019
- [j26]Jian Wang, Nikolay V. Dokholyan:
MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. J. Chem. Inf. Model. 59(6): 2509-2515 (2019) - [j25]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 Comput. Biol. 15(3) (2019) - [j24]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 Comput. Biol. 15(7) (2019) - 2017
- [j23]Jhuma Das, Andrei A. Aleksandrov, Liying Cui, Lihua He, John R. Riordan, Nikolay V. Dokholyan:
Transmembrane helical interactions in the CFTR channel pore. PLoS Comput. Biol. 13(6) (2017) - 2016
- [j22]Regina Politi, Marino Convertino, Konstantin I. Popov, Nikolay V. Dokholyan, Alexander Tropsha:
Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise. J. Chem. Inf. Model. 56(6): 1032-1041 (2016) - 2015
- [j21]Andrey Krokhotin, Kevin Houlihan, Nikolay V. Dokholyan:
iFoldRNA v2: folding RNA with constraints. Bioinform. 31(17): 2891-2893 (2015) - [j20]Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay V. Dokholyan:
ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations. PLoS Comput. Biol. 11(10) (2015) - 2013
- [j19]Feng Ding, Nikolay V. Dokholyan:
Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark. J. Chem. Inf. Model. 53(8): 1871-1879 (2013) - [j18]Denis Fourches, Eugene N. Muratov, Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha:
Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. J. Chem. Inf. Model. 53(8): 1915-1922 (2013) - 2012
- [j17]Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha:
Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening. J. Chem. Inf. Model. 52(1): 16-28 (2012) - 2011
- [j16]David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan:
Rigid substructure search. Bioinform. 27(9): 1327-1329 (2011) - [j15]Pradeep Kota, Feng Ding, Srinivas Ramachandran, Nikolay V. Dokholyan:
Gaia: automated quality assessment of protein structure models. Bioinform. 27(16): 2209-2215 (2011) - [j14]Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha:
Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets. J. Chem. Inf. Model. 51(9): 2027-2035 (2011) - [j13]Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan:
Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation. PLoS Comput. Biol. 7(1) (2011) - 2010
- [j12]Feng Ding, Shuangye Yin, Nikolay V. Dokholyan:
Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands. J. Chem. Inf. Model. 50(9): 1623-1632 (2010) - [j11]Vinal V. Lakhani, Feng Ding, Nikolay V. Dokholyan:
Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences. PLoS Comput. Biol. 6(4) (2010)
2000 – 2009
- 2009
- [j10]Srinivas Ramachandran, Adrian W. R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan:
A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1). PLoS Comput. Biol. 5(4) (2009) - 2008
- [j9]Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan:
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinform. 24(17): 1951-1952 (2008) - [j8]Shuangye Yin, Lada Biedermannová, Jirí Vondrásek, Nikolay V. Dokholyan:
MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening. J. Chem. Inf. Model. 48(8): 1656-1662 (2008) - [j7]Adrian W. R. Serohijos, Tamás Hegedüs, John R. Riordan, Nikolay V. Dokholyan:
Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding. PLoS Comput. Biol. 4(2) (2008) - [j6]Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo:
Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions. PLoS Comput. Biol. 4(7) (2008) - [j5]Jihua Hao, Adrian W. R. Serohijos, Gail Newton, Gina Tassone, Zuncai Wang, Dennis C. Sgroi, Nikolay V. Dokholyan, James P. Basilion:
Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers. PLoS Comput. Biol. 4(8) (2008) - 2006
- [j4]Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, Nikolay V. Dokholyan:
iFold: a platform for interactive folding simulations of proteins. Bioinform. 22(21): 2693-2694 (2006) - [j3]Feng Ding, Nikolay V. Dokholyan:
Emergence of Protein Fold Families through Rational Design. PLoS Comput. Biol. 2(7) (2006) - [j2]Feng Ding, Nikolay V. Dokholyan:
Correction: Emergence of Protein Fold Families through Rational Design. PLoS Comput. Biol. 2(10) (2006) - 2005
- [j1]Sagar D. Khare, Feng Ding, Kenneth N. Gwanmesia, Nikolay V. Dokholyan:
Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases. PLoS Comput. Biol. 1(3) (2005)
Coauthor Index
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