Nikolay V. Dokholyan

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 16

Top Topics

Constrained Minimization

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Debarshi Kundu, Archisman Ghosh, Srinivasan Ekambaram, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
Application of Quantum Tensor Networks for Protein Classification. CoRR (2024)
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)
Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan
Differentiable Rotamer Sampling with Molecular Force Fields. CoRR (2023)
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) (2022)
Jian Wang, Nikolay V. Dokholyan
Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. J. Chem. Inf. Model. 62 (3) (2022)
Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
Drug Discovery Approaches using Quantum Machine Learning. CoRR (2021)
Junde Li, Mahabubul Alam, Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh
Invited: Drug Discovery Approaches using Quantum Machine Learning. DAC (2021)
Congzhou M. Sha, Nikolay V. Dokholyan
Simple exponential acceleration of the power iteration algorithm. CoRR (2021)
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) (2020)
Nicholas I. Brodie, Konstantin 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)
Jian Wang, Nikolay V. Dokholyan
MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. J. Chem. Inf. Model. 59 (6) (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 Comput. Biol. 15 (7) (2019)
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)
Regina Politi, Marino Convertino, Konstantin 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) (2016)
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)
Andrey Krokhotin, Kevin Houlihan, Nikolay V. Dokholyan
iFoldRNA v2: folding RNA with constraints. Bioinform. 31 (17) (2015)
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) (2013)
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) (2013)
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) (2012)
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)
Pradeep Kota, Feng Ding, Srinivas Ramachandran, Nikolay V. Dokholyan
Gaia: automated quality assessment of protein structure models. Bioinform. 27 (16) (2011)
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) (2011)
David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan
Rigid substructure search. Bioinform. 27 (9) (2011)
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)
Feng Ding, Shuangye Yin, Nikolay V. Dokholyan
Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands. J. Chem. Inf. Model. 50 (9) (2010)
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)
Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinform. 24 (17) (2008)
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)
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) (2008)
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)
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)
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) (2006)
Feng Ding, Nikolay V. Dokholyan
Correction: Emergence of Protein Fold Families through Rational Design. PLoS Comput. Biol. 2 (10) (2006)
Feng Ding, Nikolay V. Dokholyan
Emergence of Protein Fold Families through Rational Design. PLoS Comput. Biol. 2 (7) (2006)
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)