Protein structural similarity

Koch MA, Wittenberg LO, Basu S, Jeyaraj DA, Gourzoididou E, Reinecke K, Odermatt A, Waldmann H, Compound library development guided by protein structure similarity clustering and natural product structure, Proc Natl Acad Sci USA 101 16721-16726, 2004. 

Koch MA, Breinbauer R, Waldmann H. (2003) Protein structure similarity as guiding principle for combinatorial library design. Biol. Chem. 384 1265-1272. 

Natural Product Scaffolds and Protein Structure Similarity Clustering (PSSC) as Inspiration Sources for Compound Library Design in Chemogenomics and Drug Development... 

PSSC as Guiding Principle for Compound Library Design 5.1. Protein structure similarity clustering (PSSC)... 

Figure 4. Nature s conservatism and diversity found in a protein structure similarity cluster. The conservatism found in the cluster can be used for the selection of pre-validated guiding structures for compound library design. The chemical diversity of the compound library is needed to address the biological diversity found in the binding sites of the cluster members.

The examples from literature and the hrst application of PSSC clustering in the discovery of inhibitors for proteins from the Cdc25A, AChE and 1 lfdTDSi/2 cluster convincingly demonstrates that application of target clustering based on protein structure similarity in conjunction with natural... 

In Chapter 3, the group of Prof. Herbert Waldmann at the Max Plank Institute for Molecular Physiology provides a rationale on how natural products which play historically a predominant role in drug discovery are efficiently used in combination with protein structure similarity clustering to inspire directed compound library design and target identification. 

Natural Product-derived Compound Libraries and Protein Structure Similarity... 

M.A. Koch and H. Waldmann, Protein structure similarity clustering and natural product structure as guiding principles in drug discovery. Drug Disc. Today, 2005, 10(7), 471. 

Koch, M. A., Waldmann, H. Natural product-derived compounds libraries and protein structure similarity as guiding principles for the discovery of drug candidates. In Chemogenomics in Drug Discovery A Medicinal Chemistry Perspective (Kubinyi, H., Muller, G., Eds). Wiley-VCH, 2004, pp. 377-403. 

Balamuragan, R., Dekker, F. J., Waldmann, H. Design of compound libraries based on natural product scaffolds and protein structure similarity clustering (PSSC). Mol BioSyst. 2005, 1, 36—45. 

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