Computational Design of Ligand Binding Proteins

In silico Identification and Characterization of Protein-Ligand BindingSites.- Computational Modeling of Small Molecule Ligand Binding Interactionsand Affinities.- Binding Site Prediction of Proteins with Organic Compounds orPeptides Using GALAXY Web Servers.- Rosetta and the Design of Ligand Binding Sites.-PocketOptimizer and the Design of Ligand Binding Sites.- Proteus and the Designof Ligand Binding Sites.- A Structure Based Design Protocol for OptimizingCombinatorial Protein Libraries.- Combined and Iterative Use of ComputationalDesign and Directed Evolution for Protein-Ligand Binding Design.- ImprovingBinding Affinity and Selectivity of Computationally Designed Ligand BindingProteins Using Experiments.- Computational Design of MultinuclearMetalloproteins Using Unnatural Amino Acids.- De Novo Design ofMetalloproteins and Metalloenzymes in a Three-helix Bundle.- Design ofLight-Controlled Protein Conformations and Functions.- ComputationalIntroduction of Catalytic Activity into Proteins.- Generating High AccuracyPeptide Binding Data in High Throughput with Yeast Surface Display andSORTCERY.- Design of Specific Peptide-Protein Recognition.- Computational Designof DNA-binding Proteins.- Motif-driven Design of Protein-Protein Interfaces.- ComputationalReprogramming of T Cell Antigen Receptor Binding Properties.- ComputationalModeling of T Cell Receptor Complexes.- Computational Design of ProteinLinkers.- Modeling of Protein-RNA Complex Structures Using ComputationalDocking Methods.