Nikolay V. Dokholyan

39 papers A* 1Journal 37Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Multimodal Bond Reconstruction toward Generative Molecular Design. J. Chem. Inf. Model. Jian Wang, Nikolay V. Dokholyan
2025	J	`jnl`	Leveraging Transfer Learning for Predicting Protein-Small-Molecule Interaction Predictions. J. Chem. Inf. Model. Jian Wang, Nikolay V. Dokholyan
2024	—	`conf`	Application of Quantum Tensor Networks for Protein Classification. ACM Great Lakes Symposium on VLSI Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
2024	J	`jnl`	Application of Quantum Tensor Networks for Protein Classification. CoRR Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
2024	J	`jnl`	Differentiable rotamer sampling with molecular force fields. Briefings Bioinform. Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan
2024	J	`jnl`	Quantifying network behavior in the rat prefrontal cortex. Frontiers Comput. Neurosci. Congzhou M. Sha, Jian Wang, Richard B. Mailman, Yang Yang, Nikolay V. Dokholyan
2023	J	`jnl`	Differentiable Rotamer Sampling with Molecular Force Fields. CoRR Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan
2022	J	`jnl`	Predicting Protein-Ligand Docking Structure with Graph Neural Network. J. Chem. Inf. Model. Huaipan Jiang, Jian Wang, Weilin Cong, Yihe Huang, Morteza Ramezani, Anup Sarma, Nikolay V. Dokholyan, Mehrdad Mahdavi, Mahmut T. Kandemir
2022	J	`jnl`	Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. J. Chem. Inf. Model. Jian Wang, Nikolay V. Dokholyan
2021	J	`jnl`	Drug Discovery Approaches using Quantum Machine Learning. CoRR Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
2021	A*	`conf`	Invited: Drug Discovery Approaches using Quantum Machine Learning. DAC Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
2021	J	`jnl`	Simple exponential acceleration of the power iteration algorithm. CoRR Congzhou M. Sha, Nikolay V. Dokholyan
2020	J	`jnl`	Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. J. Chem. Inf. Model. Huaipan Jiang, Mengran Fan, Jian Wang, Anup Sarma, Shruti Mohanty, Nikolay V. Dokholyan, Mehrdad Mahdavi, Mahmut T. Kandemir
2019	J	`jnl`	Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. PLoS Comput. Biol. Nicholas I. Brodie, Konstantin I. Popov, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers
2019	J	`jnl`	MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. J. Chem. Inf. Model. Jian Wang, Nikolay V. Dokholyan
2019	J	`jnl`	β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology. PLoS Comput. Biol. Elizabeth A. Proctor, David D. Mowrey, Nikolay V. Dokholyan
2017	J	`jnl`	Transmembrane helical interactions in the CFTR channel pore. PLoS Comput. Biol. Jhuma Das, Andrei A. Aleksandrov, Liying Cui, Lihua He, John R. Riordan, Nikolay V. Dokholyan
2016	J	`jnl`	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. Regina Politi, Marino Convertino, Konstantin I. Popov, Nikolay V. Dokholyan, Alexander Tropsha
2015	J	`jnl`	ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations. PLoS Comput. Biol. Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay V. Dokholyan
2015	J	`jnl`	iFoldRNA v2: folding RNA with constraints. Bioinform. Andrey Krokhotin, Kevin Houlihan, Nikolay V. Dokholyan
2013	J	`jnl`	Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark. J. Chem. Inf. Model. Feng Ding, Nikolay V. Dokholyan
2013	J	`jnl`	Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. J. Chem. Inf. Model. Denis Fourches, Eugene N. Muratov, Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha
2012	J	`jnl`	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. Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha
2011	J	`jnl`	Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets. J. Chem. Inf. Model. Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha
2011	J	`jnl`	Gaia: automated quality assessment of protein structure models. Bioinform. Pradeep Kota, Feng Ding, Srinivas Ramachandran, Nikolay V. Dokholyan
2011	J	`jnl`	Rigid substructure search. Bioinform. David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan
2011	J	`jnl`	Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation. PLoS Comput. Biol. Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan
2010	J	`jnl`	Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences. PLoS Comput. Biol. Vinal V. Lakhani, Feng Ding, Nikolay V. Dokholyan
2010	J	`jnl`	Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands. J. Chem. Inf. Model. Feng Ding, Shuangye Yin, Nikolay V. Dokholyan
2009	J	`jnl`	A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1). PLoS Comput. Biol. Srinivas Ramachandran, Adrian W. R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan
2008	J	`jnl`	Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions. PLoS Comput. Biol. Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo
2008	J	`jnl`	Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding. PLoS Comput. Biol. Adrian W. R. Serohijos, Tamás Hegedüs, John R. Riordan, Nikolay V. Dokholyan
2008	J	`jnl`	Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers. PLoS Comput. Biol. Jihua Hao, Adrian W. R. Serohijos, Gail Newton, Gina Tassone, Zuncai Wang, Dennis C. Sgroi, Nikolay V. Dokholyan, James P. Basilion
2008	J	`jnl`	MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening. J. Chem. Inf. Model. Shuangye Yin, Lada Biedermannová, Jirí Vondrásek, Nikolay V. Dokholyan
2008	J	`jnl`	iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinform. Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan
2006	J	`jnl`	Correction: Emergence of Protein Fold Families through Rational Design. PLoS Comput. Biol. Feng Ding, Nikolay V. Dokholyan
2006	J	`jnl`	Emergence of Protein Fold Families through Rational Design. PLoS Comput. Biol. Feng Ding, Nikolay V. Dokholyan
2006	J	`jnl`	iFold: a platform for interactive folding simulations of proteins. Bioinform. Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, Nikolay V. Dokholyan
2005	J	`jnl`	Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases. PLoS Comput. Biol. Sagar D. Khare, Feng Ding, Kenneth N. Gwanmesia, Nikolay V. Dokholyan