Methods in Protein Design

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