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 I
