Table of Contents

- Computational Design of Novel Protein Binders and Experimental Affinity Maturation - Mining Tertiary Structural Motifs for Assessment of Designability - Computational Methods for Controlling Binding Specificity - Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations - OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms - Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement - Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins - Multi-State Protein Design Using CLEVER and CLASSY - Using Analyses of Amino Acid Coevolution to Understand Protein Structure and Function - Evolution Based Design of Proteins - Protein Engineering and Stabilization from Sequence Statistics: Variation and Co-Variation Analysis - Enzyme Engineering by Targeted Libraries - Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping - Engineering Fibronectin-Based Binding Proteins by Yeast Surface Display - Engineering and Analysis of Peptide-Recognition Domain Specificities by Phage Display and Deep Sequencing - Efficient Sampling of SCHEMA Chimera Families to Identify Useful Sequence Elements - Protein Switch Engineering by Domain Insertion - Design of Chimeric Proteins by Combination of Subdomain-Sized Fragments - α-Helix Mimicry with α/β-Peptides