Modeling of protein-RNA complex structures using computational docking methods / Bharat Madan [and six others]. Computational modeling of small molecule ligand binding interactions and affinities / Marino Convertino and Nikolay V. Dokholyan -- Binding site prediction of proteins with organic compounds or peptides using GALAXY web servers / Lim Heo [and three others] -- Rosetta and the Design of Ligand Binding Sites / Rocco Moretti [and three others] -- PocketOptimizer and the design of ligand binding sites / Andre C. Stiel, Mehdi Nellen, and Birte HoĢcker -- Proteus and the design of ligand binding sites / Savvas Polydorides [and five others] -- A structure-based design protocol for optimizing combinatorial protein libraries / Mark W. Lunt and Christopher D. Snow -- Combined and iterative use of computational design and directed evolution for protein-ligand binding design / Meng Wang and Huimin Zhao -- Improving binding affinity and selectivity of computationally designed ligand-binding proteins using experiments / Christine E. Tinberg and Sagar D. Khare -- Computational design of multinuclear metalloproteins using unnatural amino acids / William A. Hansen, Jeremy H. Mills, and Sagar D. Khare -- De novo design of metalloproteins and metalloenzymes in a three-helix bundle / Jefferson S. Plegaria and Vincent L. Pecoraro -- Design of light-controlled protein conformations and functions / Ryan S. Ritterson [and three others] -- Computational introduction of catalytic activity into proteins / Steve J. Bertolani, Dylan Alexander Carlin, and Justin B. Siegel -- Generating high-accuracy peptide-binding data in high throughput with yeast surface display and SORTCERY / Lothar Luther Reich, Sanjib Dutta, and Amy E. Keating -- Design of specific peptide-protein recognition / Fan Zheng and Gevorg Grigoryan -- Computational design of DNA-binding proteins / Summer Thyme and Yifan Song -- Motif-driven design of protein-protein interfaces / Daniel-Adriano Silva, Bruno E. Correia, and Erik Procko -- Computational reprogramming of T cell antigen receptor binding properties / Timothy P. Riley [and four others] -- Computational modeling of T cell receptor complexes / Timothy P. Riley [and four others] -- Computational design of protein linkers / Brian Kuhlman, Tim Jacobs, and Tom Linskey -- Modeling of protein-RNA complex structures using computational docking methods / Bharat Madan [and six others].
Summary:
This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.