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Part I Methods to Discover and Characterize Ligands for Targets and/or Ligases. 1. Protein Ligand Interactions Using Surface Plasmon Resonance Nichole O’Connell 2. High-Throughput Detection of Ligand-Protein Binding using a SplitLuc Cellular Thermal Shift Assay Tino W. Sanchez, Ashley Owens, Natalia J. Martinez, Eric Wallgren, Anton Simeonov, and Mark J. Henderson 3. Proteins and their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3 Danielle Allison Brackenridge and Liam James McGuffin 4. Evaluating ligands for ubiquitin ligases using affinity beads Jennifer Dobrodziej, Hanqing Dong, Kurt Zimmermann, and Christopher M. Hickey Part II Approaches to Study Ligase:Degrader:Target Ternary Complexes. 5. Mechanistic and Structural Features of PROTAC Ternary Complexes Ryan Casement, Adam Bond, Conner Craigon, and Alessio Ciulli 6. MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding In Drug Development Tanja Bortoschik, Andreas Zoephel, Klaus Rumpel, Alessio Ciulli, and Charles Heffern 7. An in vitro Pull-down Assay of the E3 ligase:PROTAC:Substrate Ternary Complex to Identify Effective PROTACs Daniel P. Bondeson, Blake E. Smith, and Alexandru D. Buhimschi 8. Kinetic detection of E3: PROTAC: Target Ternary Complexes using NanoBRET technology in Live Cells Sarah D. Mahan, Kristin M. Riching, Marjeta Urh, and Danette L. Daniels Part III Approaches and Tools to Understand Ubiquitylation and Proteasomal Degradation 9. Inducing Ubiquitylation and Protein Degradation as a Drug Development Strategy Kamaldeep S. Dhami and XiaoDong Huang 10. Methodological Versatility of Tandem Ubiquitin Binding Entities (TUBEs) for Understanding Poly-ubiquitination and its Various Chains Katie J. Sheets, Patrick H. Gross, Myra J. Zerr, and Dahmane Ouazia, and Karteek Kadimisetty 11. Global Mass Spectrometry-Based Analysis of Protein Ubiquitination Using K-e-GG Remnant Antibody Enrichment Alissa J. Nelson, Yiying Zhu, Jian Min Ren, and Matthew P. Stokes 12. Determination of Proteasomal Unfolding Ability by Christina M. Hurley and Daniel A. Kraut Part IV Methods for Evaluating Protein Degrader Function 13. Methods for Quantitative Assessment of Protein Degradation Radoslaw P. Nowak, Hong Yue, Emily Y. Park, and Eric S. Fischer 14. A High Throughput method to prioritize PROTAC intracellular target engagement and cell permeability using NanoBRET by James D. Vasta, Cesear R. Corona, and Matthew B. Robers 15. Profiling CELMoD Mediated Degradation of Cereblon Neosubstrates by Joel W. Thompson, Thomas Clayton, Gody Khambatta, Leslie A. Bateman, Christopher W. Carroll, Philip P. Chamberlain, and Mary E. Matyskiela 16. Global Proteome Profiling to Assess Changes in Protein Abundance using Isobaric Labeling and Liquid Chromatography Tandem Mass Spectrometry by Anthony P. Possemato, Kathryn Abell, and Matthew P. Stokes 17. PHOTACs Enable Optical Control of Protein Degradation by Martin Reynders and Dirk Trauner 18. Protocols for synthesis of SNIPERs and the methods to evaluate the anti-cancer affects by Yoshinori Tsukumo, Genichiro Tsuji, Hidetomo Yokoo,Norihito Shibata, Nobumichi Ohoka, Yosuke Demizu, and Mikihiko Naito

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