Titlebook: Rational Drug Design; Methods and Protocol Yi Zheng Book 2012 Springer Science+Business Media New York 2012 ATP binding.GTPases.Structure b

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Affinity Purification of Protein Kinases that Adopt a Specific Inactive Conformation,irements for adopting this conformation are still poorly understood. Here, we describe a general method for enriching DFG-out adopting kinases from cell lysates with an affinity resin that contains a general ligand that specifically recognizes this inactive form.

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On Setting Up and Assessing Docking Simulations for Virtual Screening,lining experimental efforts in that regard. In this chapter, we describe specific software packages and protocols that can be used to efficiently set up a computational screening using a library of compounds and a docking program. We also discuss consensus- and clustering-based approaches that can b

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Rational Design of Rho GTPase-Targeting Inhibitors, Virtual screening of compounds that fit into surface grooves of RhoA known to be critical for guanine nucleotide exchange factor (GEF) interaction produced chemical candidates with minimized docking energy. Subsequent screening for inhibitory activity of RhoA binding to the Rho-GEF, LARG, identifie

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Rational Design of Peptide Ligands Against a Glycolipid by NMR Studies,e GD2 and of GD2 bound to anti-GD2 mAb 3F8 were resolved by saturation transfer difference nuclear magnetic resonance and molecular modeling. Then small molecule cyclic peptide ligands that bind to GD2 selectively were designed, and shown to affect GD2-mediated signal transduction. The solution stru

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Identification of Allosteric Inhibitors of p21-Activated Kinase,cuous inhibition of additional unintended kinase targets. Allosteric inhibitors that target less conserved regions of protein kinases represent an alternative approach that may provide more selective kinase inhibition. In this report, protocols are provided for the screening and identification of Pa

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Using a Modified Yeast Two-Hybrid System to Screen for Chemical GEF Inhibitors,that over-activation of Ras-like pathways participates in the development of many cancer types. In particular, GTPases of the Rho family control cell adhesion, survival, motility, and invasion, cell properties dysregulated in most cancer types. Rho activation is triggered by RhoGEFs, most of which f

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Random Mutagenesis of Peptide Aptamers as an Optimization Strategy for Inhibitor Screening,pplied to a variety of different targets. Because of the screening method in cells and the highly combinatorial libraries available, this approach yields rapidly highly specific candidate inhibitors. Once a hit peptide has been identified, its interaction strength and affinity towards its target pro

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