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)

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)

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)

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)

Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. - Praveen Nedumpully-Govindan; Lin Li 003; Emil Alexov; Mark A. Blenner; Feng Ding 002 (Bioinform., 2014)

CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection. - Praveen Nedumpully-Govindan; Domen B. Jemec; Feng Ding 002 (J. Chem. Inf. Model., 2016)

Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau. - Huan He; Yuying Liu; Yunxiang Sun; Feng Ding 002 (J. Chem. Inf. Model., 2021)

Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD128-38 and Absence in Nontoxic Glycine Mutants. - Yunxiang Sun; Junchao Huang; Xiangmei Duan; Feng Ding 002 (J. Chem. Inf. Model., 2021)

Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation. - Huayuan Tang; Yunxiang Sun; Feng Ding 002 (J. Chem. Inf. Model., 2022)

Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. - Yuying Liu; Ying Wang; Yu Zhang; Yu Zou; Guanghong Wei; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2023)

Dissecting the Self-assembly Dynamics of Imperfect Repeats in α-Synuclein. - Fengjuan Huang; Ying Wang; Yu Zhang; Chuang Wang 013; Jiangfang Lian; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2023)

SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges. - Ying Wang; Jia Xu; Fengjuan Huang; Jiajia Yan; Xinjie Fan; Yu Zou; Chuang Wang 013; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2023)

Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth. - Gangtong Huang; Huayuan Tang; Yuying Liu; Chi Zhang; Pu Chun Ke; Yunxiang Sun; Feng Ding 002 (J. Chem. Inf. Model., 2023)

Unveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations. - Fengjuan Huang; Xinjie Fan; Ying Wang; Chuang Wang 013; Yu Zou; Jiangfang Lian; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2023)

Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes. - Xinjie Fan; Xiaohan Zhang; Jiajia Yan; Huan Xu; Wenhui Zhao; Feng Ding 002; Fengjuan Huang; Yunxiang Sun (J. Chem. Inf. Model., 2024)

Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin. - Fengjuan Huang; Jiahui Huang; Jiajia Yan; Yuying Liu; Jiangfang Lian; Qinxue Sun; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2024)

Deciphering the Morphological Difference of Amyloid-β Fibrils in Familial and Sporadic Alzheimer's Diseases. - Gangtong Huang; Zhiyuan Song; Yun Xu; Yunxiang Sun; Feng Ding 002 (J. Chem. Inf. Model., 2024)

Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation. - Fengjuan Huang; Jiajia Yan; Huan Xu; Ying Wang; Xiaohan Zhang; Yu Zou; Jiangfang Lian; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2024)

Uncovering Intermolecular Interactions Driving the Liquid-Liquid Phase Separation of the TDP-43 Low-Complexity Domain via Atomistic Dimerization Simulations. - Huayuan Tang; Yunxiang Sun; Lei Wang; Pu Chun Ke; Feng Ding 002 (J. Chem. Inf. Model., 2024)

Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease. - Fengjuan Huang; Xinjie Fan; Ying Wang; Yu Zou; Jiangfang Lian; Chuang Wang 013; Feng Ding 002; Yunxiang Sun (Briefings Bioinform., 2024)

The Glycine-Rich Region as a Flexible Molecular Glue Promoting hPrP106-145 Aggregation into β-Sheet Structures. - Xiaohan Zhang; Huan Xu; Huayuan Tang; Zhongyue Lv; Yu Zou; Fengjuan Huang; Feng Ding 002; Yunxiang Sun (J. Chem. Inf. Model., 2025)