1/29/2024 0 Comments Rigid protein scaffoldStructural organization of the endoplasmic reticulum. Cryo-electron tomography of Neurospora mitochondria. Whitehead TA, Chevalier A, Song Y et al (2012) Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. doi: 10.1016/j.jmb.2011.09.031Ĭooper S, Khatib F, Treuille A et al (2010) Predicting protein structures with a multiplayer online game. doi: 10.1126/science.1209368įleishman SJ, Whitehead TA, Strauch E-M et al (2011) Community-wide assessment of protein-interface modeling suggests improvements to design methodology. doi: 10.1016/j.jmb.2011.10.003Īzoitei ML, Correia BE, Ban Y-EA et al (2011) Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. doi: 10.1016/j.str.2010.06.010Īzoitei ML, Ban Y-EA, Julien J-P et al (2012) Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. doi: 10.1073/pnas.1004728107Ĭorreia BE, Ban Y-EA, Holmes MA et al (2010) Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Ofek G, Guenaga FJ, Schief WR et al (2010) Elicitation of structure-specific antibodies by epitope scaffolds. Savkur RS, Burris TP (2004) The coactivator LXXLL nuclear receptor recognition motif. Wärnmark A, Treuter E, Gustafsson J-A et al (2002) Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. doi: 10.1146/annurev.biochem.77.062906.171838įleishman SJ, Leaver-Fay A, Corn JE et al (2011) RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. Leaver-Fay A, Tyka M, Lewis SM et al (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Procko E, Berguig GY, Shen BW et al (2014) A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. doi: 10.1016/j.jmb.2013.06.035įleishman SJ, Whitehead TA, Ekiert DC et al (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Procko E, Hedman R, Hamilton K et al (2013) Computational design of a protein-based enzyme inhibitor. In these protocols, a motif of known structure that interacts with the target site is grafted into a scaffold protein, followed by design of the surrounding interaction surface. In order to make some of these methods more accessible, we present detailed descriptions and examples of ROSETTA computational protocols for the design of functional protein binders using seeded protein interface design. Although attractive, these computational tools carry a steep learning curve. In recent years, computational protein design has emerged as a tool for designing novel protein–protein interactions with functional relevance. The ability to accurately control and regulate these molecular interactions is of major interest for biomedical and synthetic biology applications, as well as to address fundamental biological questions. Protein–protein interfaces regulate many critical processes for cellular function.
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