The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation. - Jin Liu 005; Ruth Nussinov (PLoS Comput. Biol., 2009)

2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes. - Ruifeng Liu; Jin Liu 005; Gregory J. Tawa; Anders Wallqvist (J. Chem. Inf. Model., 2012)

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase. - Daniel R. Ripoll; Ilja V. Khavrutskii; Sidhartha Chaudhury; Jin Liu 005; Robert A. Kuschner; Anders Wallqvist; Jaques Reifman (PLoS Comput. Biol., 2012)

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. - Robert Kalescky; Hongyu Zhou; Jin Liu 005; Peng Tao 001 (PLoS Comput. Biol., 2016)

Allostery: An Overview of Its History, Concepts, Methods, and Applications. - Jin Liu 005; Ruth Nussinov (PLoS Comput. Biol., 2016)

Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps. - Hamed S. Hayatshahi; Emilio Ahuactzin; Peng Tao 001; Shouyi Wang; Jin Liu 005 (J. Chem. Inf. Model., 2019)

Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease. - Zhicheng Zuo; Jin Liu 005 (J. Chem. Inf. Model., 2019)

Allosteric Modulation of Small Molecule Drugs on ACE2 Conformational Change upon Binding to SARS-CoV-2 Spike Protein. - Duen-Shian Wang; Hamed S. Hayatshahi; Vindi M. Jayasinghe-Arachchige; Jin Liu 005 (BIBM, 2021)

Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes. - Hamed S. Hayatshahi; Robert R. Luedtke; Michelle Taylor; Peng-Jen Chen; Benjamin E. Blass; Jin Liu 005 (J. Chem. Inf. Model., 2021)

Sparse group selection and analysis of function-related residue for protein-state recognition. - Fangyun Bai; Kin Ming Puk; Jin Liu 005; Hongyu Zhou; Peng Tao 001; Wenyong Zhou; Shouyi Wang (J. Comput. Chem., 2022)

Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. - Yazdan Maghsoud; Vindi M. Jayasinghe-Arachchige; Pratibha Kumari 003; G. Andrés Cisneros; Jin Liu 005 (J. Chem. Inf. Model., 2023)

Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum. - Sita Sirisha Madugula; Pranav Pujar; Bharani Nammi; Shouyi Wang; Vindi M. Jayasinghe-Arachchige; Tyler Pham; Dominic Mashburn; Maria Artiles; Jin Liu 005 (J. Chem. Inf. Model., 2024)