Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed? von You, Wanli, Tang, Zhiye, Chang, Chia-en A

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Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems von Allec, Sarah I, Sun, Yijing, Sun, Jianan, Chang, Chia-en A, Wong, Bryan M

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Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition von Tang, Zhiye, Chang, Chia-en A

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Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment von Kaushik, Shivansh, Hung, Ta I, Chang, Chia‐en A.

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Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces von Cholko, Timothy, Chang, Chia-en A

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Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics von Chen, Wei, He, Huan, Wang, Jing, Wang, Jiahui, Chang, Chia-en A

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Amyloid‑β (Aβ42) Peptide Aggregation Rate and Mechanism on Surfaces with Widely Varied Properties: Insights from Brownian Dynamics Simulations von Cholko, Timothy, Barnum, Joseph, Chang, Chia-en A

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Dynamics and molecular interactions of single-stranded DNA in nucleic acid biosensors with varied surface properties von Cholko, Timothy, Kaushik, Shivansh, Chang, Chia-en A

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Discovery of antimicrobial agent targeting tryptophan synthase von Bosken, Yuliana K., Ai, Rizi, Hilario, Eduardo, Ghosh, Rittik K., Dunn, Michael F., Kan, Shih‐Hsin, Niks, Dimitri, Zhou, Huanbin, Ma, Wenbo, Mueller, Leonard J., Fan, Li, Chang, Chia‐En A.

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Ligand configurational entropy and protein binding von Chang, Chia-en A, Chen, Wei, Gilson, Michael K

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Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand–Protein Recognition and Compound Design von Tang, Zhiye, Chen, Si-Han, Chang, Chia-en A

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Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors von You, Wanli, Chang, Chia-en A

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Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis von Gao, Yingning, Roberts, Christopher C., Toop, Aaron, Chang, Chia-en A., Wheeldon, Ian

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Discovery of CDK8/CycC Ligands with a New Virtual Screening Tool von Chen, Wei, Ren, Xiaodong, Chang, Chia‐en A.

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Ligand Binding Pathways and Conformational Transitions of the HIV Protease von Miao, Yinglong, Huang, Yu-ming M, Walker, Ross C, McCammon, J. Andrew, Chang, Chia-en A

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Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes von Ruzmetov, Talant, Montes, Ruben, Sun, Jianan, Chen, Si-Han, Tang, Zhiye, Chang, Chia-en A.

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What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks von Hung, Ta I, Hsieh, Yun-Jung, Lu, Wei-Lin, Wu, Kuen-Phon, Chang, Chia-En A

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Inhibiting Matrix Metalloproteinase‑2 Activation by Perturbing Protein–Protein Interactions Using a Cyclic Peptide von Sarkar, Priyanka, Li, Zhonghan, Ren, Wendan, Wang, Siwen, Shao, Shiqun, Sun, Jianan, Ren, Xiaodong, Perkins, Nicole G, Guo, Zhili, Chang, Chia-En A, Song, Jikui, Xue, Min

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Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis von Zhang, Chunhua, Brown, Michelle Q., van de Ven, Wilhelmina, Zhang, Zhi-Min, Wu, Bin, Young, Michael C., Synek, Lukáš, Borchardt, Dan, Harrison, Reed, Pan, Songqin, Luo, Nan, Huang, Yu-ming M., Ghang, Yoo-Jin, Ung, Nolan, Li, Ruixi, Isley, Jonathan, Morikis, Dimitrios, Song, Jikui, Guo, Wei, Hooley, Richard J., Chang, Chia-en A., Yang, Zhenbiao, Zarsky, Viktor, Muday, Gloria K., Hicks, Glenn R., Raikhel, Natasha V.

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GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems von Cholko, Timothy, Kaushik, Shivansh, Wu, Kingsley Y., Montes, Ruben, Chang, Chia-en A.

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