Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases. - Sagar D. Khare; Feng Ding 002; Kenneth N. Gwanmesia; Nikolay V. Dokholyan (PLoS Comput. Biol., 2005)

iFold: a platform for interactive folding simulations of proteins. - Shantanu Sharma 002; Feng Ding 002; Huifen Nie; Daniel Watson; Aditya Unnithan; Jameson Lopp; Diane Pozefsky; Nikolay V. Dokholyan (Bioinform., 2006)

Emergence of Protein Fold Families through Rational Design. - Feng Ding 002; Nikolay V. Dokholyan (PLoS Comput. Biol., 2006)

Correction: Emergence of Protein Fold Families through Rational Design. - Feng Ding 002; Nikolay V. Dokholyan (PLoS Comput. Biol., 2006)

iFoldRNA: three-dimensional RNA structure prediction and folding. - Shantanu Sharma 002; Feng Ding 002; Nikolay V. Dokholyan (Bioinform., 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)

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)

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)

Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions. - Denise G. Teotico; Monica L. Frazier; Feng Ding 002; Nikolay V. Dokholyan; Brenda R. S. Temple; Matthew R. Redinbo (PLoS Comput. Biol., 2008)

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)

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands. - Feng Ding 002; Shuangye Yin; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2010)

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences. - Vinal V. Lakhani; Feng Ding 002; Nikolay V. Dokholyan (PLoS Comput. Biol., 2010)

Gaia: automated quality assessment of protein structure models. - Pradeep Kota; Feng Ding 002; Srinivas Ramachandran; Nikolay V. Dokholyan (Bioinform., 2011)

Rigid substructure search. - David Shirvanyants; Anastassia N. Alexandrova; Nikolay V. Dokholyan (Bioinform., 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)

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)

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)

Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark. - Feng Ding 002; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2013)

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. - Denis Fourches; Eugene N. Muratov; Feng Ding 002; Nikolay V. Dokholyan; Alexander Tropsha (J. Chem. Inf. Model., 2013)

iFoldRNA v2: folding RNA with constraints. - Andrey Krokhotin; Kevin Houlihan; Nikolay V. Dokholyan (Bioinform., 2015)

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations. - Benfeard Williams II; Marino Convertino; Jhuma Das; Nikolay V. Dokholyan (PLoS Comput. Biol., 2015)

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)

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)

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. - Jian Wang 094; Nikolay V. Dokholyan (J. Chem. Inf. Model., 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)

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)

Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. - Huaipan Jiang; Mengran Fan; Jian Wang 094; Anup Sarma; Shruti Mohanty; Nikolay V. Dokholyan; Mehrdad Mahdavi; Mahmut T. Kandemir (J. Chem. Inf. Model., 2020)

Invited: Drug Discovery Approaches using Quantum Machine Learning. - Junde Li; Mahabubul Alam; Congzhou M. Sha; Jian Wang 094; Nikolay V. Dokholyan; Swaroop Ghosh (DAC, 2021)

Drug Discovery Approaches using Quantum Machine Learning. - Junde Li; Mahabubul Alam; Congzhou M. Sha; Jian Wang 094; Nikolay V. Dokholyan; Swaroop Ghosh (CoRR, 2021)

Simple exponential acceleration of the power iteration algorithm. - Congzhou M. Sha; Nikolay V. Dokholyan (CoRR, 2021)

Predicting Protein-Ligand Docking Structure with Graph Neural Network. - Huaipan Jiang; Jian Wang 094; Weilin Cong; Yihe Huang; Morteza Ramezani; Anup Sarma; Nikolay V. Dokholyan; Mehrdad Mahdavi; Mahmut T. Kandemir (J. Chem. Inf. Model., 2022)

Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. - Jian Wang 094; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2022)

Application of Quantum Tensor Networks for Protein Classification. - Debarshi Kundu; Archisman Ghosh; Srinivasan Ekambaram; Jian Wang 094; Nikolay V. Dokholyan; Swaroop Ghosh (ACM Great Lakes Symposium on VLSI, 2024)

Differentiable rotamer sampling with molecular force fields. - Congzhou M. Sha; Jian Wang 094; Nikolay V. Dokholyan (Briefings Bioinform., 2024)

Quantifying network behavior in the rat prefrontal cortex. - Congzhou M. Sha; Jian Wang 094; Richard B. Mailman; Yang Yang; Nikolay V. Dokholyan (Frontiers Comput. Neurosci., 2024)

Leveraging Transfer Learning for Predicting Protein-Small-Molecule Interaction Predictions. - Jian Wang 094; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2025)