Nikolay V. Dokholyan

According to our database, Nikolay V. Dokholyan authored at least 36 papers between 2005 and 2025.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2025

Leveraging Transfer Learning for Predicting Protein-Small-Molecule Interaction Predictions.

Jian Wang, Nikolay V. Dokholyan

J. Chem. Inf. Model., 2025

2024

Quantifying network behavior in the rat prefrontal cortex.

Congzhou M. Sha, Jian Wang, Richard B. Mailman, Yang Yang, Nikolay V. Dokholyan

Frontiers Comput. Neurosci., 2024

Differentiable rotamer sampling with molecular force fields.

Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan

Briefings Bioinform., 2024

Application of Quantum Tensor Networks for Protein Classification.

Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh

Proceedings of the Great Lakes Symposium on VLSI 2024, 2024

2022

Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction.

Jian Wang, Nikolay V. Dokholyan

J. Chem. Inf. Model., 2022

Predicting Protein-Ligand Docking Structure with Graph Neural Network.

Huaipan Jiang, Jian Wang, Weilin Cong, Yihe Huang, Morteza Ramezani, Anup Sarma, Nikolay V. Dokholyan, Mehrdad Mahdavi, Mahmut T. Kandemir

J. Chem. Inf. Model., 2022

2021

Simple exponential acceleration of the power iteration algorithm.

Congzhou M. Sha, Nikolay V. Dokholyan

CoRR, 2021

Drug Discovery Approaches using Quantum Machine Learning.

Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh

CoRR, 2021

Invited: Drug Discovery Approaches using Quantum Machine Learning.

Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh

Proceedings of the 58th ACM/IEEE Design Automation Conference, 2021

2020

Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks.

Huaipan Jiang, Mengran Fan, Jian Wang, Anup Sarma, Shruti Mohanty, Nikolay V. Dokholyan, Mehrdad Mahdavi, Mahmut T. Kandemir

J. Chem. Inf. Model., 2020

2019

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology.

Elizabeth A. Proctor, David D. Mowrey, Nikolay V. Dokholyan

PLoS Comput. Biol., 2019

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

Nicholas I. Brodie, Konstantin I. Popov, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers

PLoS Comput. Biol., 2019

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints.

Jian Wang, Nikolay V. Dokholyan

J. Chem. Inf. Model., 2019

2017

Transmembrane helical interactions in the CFTR channel pore.

Jhuma Das, Andrei A. Aleksandrov, Liying Cui, Lihua He, John R. Riordan, Nikolay V. Dokholyan

PLoS Comput. Biol., 2017

2016

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.

Regina Politi, Marino Convertino, Konstantin I. Popov, Nikolay V. Dokholyan, Alexander Tropsha

J. Chem. Inf. Model., 2016

2015

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.

Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay V. Dokholyan

PLoS Comput. Biol., 2015

iFoldRNA v2: folding RNA with constraints.

Andrey Krokhotin, Kevin Houlihan, Nikolay V. Dokholyan

Bioinform., 2015

2013

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches.

Denis Fourches, Eugene N. Muratov, Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha

J. Chem. Inf. Model., 2013

Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark.

Feng Ding, Nikolay V. Dokholyan

J. Chem. Inf. Model., 2013

2012

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.

Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha

J. Chem. Inf. Model., 2012

2011

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation.

Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan

PLoS Comput. Biol., 2011

Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets.

Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha

J. Chem. Inf. Model., 2011

Rigid substructure search.

David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan

Bioinform., 2011

Gaia: automated quality assessment of protein structure models.

Pradeep Kota, Feng Ding, Srinivas Ramachandran, Nikolay V. Dokholyan

Bioinform., 2011

2010

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences.

Vinal V. Lakhani, Feng Ding, Nikolay V. Dokholyan

PLoS Comput. Biol., 2010

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands.

Feng Ding, Shuangye Yin, Nikolay V. Dokholyan

J. Chem. Inf. Model., 2010

2009

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1).

Srinivas Ramachandran, Adrian W. R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan

PLoS Comput. Biol., 2009

2008

Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions.

Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo

PLoS Comput. Biol., 2008

Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding.

Adrian W. R. Serohijos, Tamás Hegedüs, John R. Riordan, Nikolay V. Dokholyan

PLoS Comput. Biol., 2008

Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers.

Jihua Hao, Adrian W. R. Serohijos, Gail Newton, Gina Tassone, Zuncai Wang, Dennis C. Sgroi, Nikolay V. Dokholyan, James P. Basilion

PLoS Comput. Biol., 2008

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening.

Shuangye Yin, Lada Biedermannová, Jirí Vondrásek, Nikolay V. Dokholyan

J. Chem. Inf. Model., 2008

iFoldRNA: three-dimensional RNA structure prediction and folding.

Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan

Bioinform., 2008

2006

Correction: Emergence of Protein Fold Families through Rational Design.

Feng Ding, Nikolay V. Dokholyan

PLoS Comput. Biol., 2006

Emergence of Protein Fold Families through Rational Design.

Feng Ding, Nikolay V. Dokholyan

PLoS Comput. Biol., 2006

iFold: a platform for interactive folding simulations of proteins.

Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, Nikolay V. Dokholyan

Bioinform., 2006

2005

Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases.

Sagar D. Khare, Feng Ding, Kenneth N. Gwanmesia, Nikolay V. Dokholyan

PLoS Comput. Biol., 2005