Andrew Perry

Chemical Biology & Drug Design, Vol. 73, No. 2. (2009), pp. 157-167. Harnessing data from the growing number of protein-ligand complexes in the Protein Data Bank is an important task in drug discovery. In order to benefit from the abundance of three-dimensional structures, structural data must be integrated with sequence as well as chemical data and the protein-small molecule interactions characterized structurally at the inter-atomic level. In this study, we present CREDO, a new publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its application programming interface. Features of CREDO include implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Selected analyses of these key features are presented to... - Andrew Perry

Code and docs are here: http://mordred.bioc.cam.ac.uk/trac... - Andrew Perry

I see it at Qik, but just black here? - Neil Saunders

Looks like a bug ... not sure if it's FriendFeed or Qiks responsibility. - Andrew Perry

Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffraction data using MOLREP and Phaser. This method has recently been shown to be generally applicable with improved MR performance demonstrated for eight NMR structures refined using Rosetta (Qian et al., Nature 2007;450:259-264). Additionally, NMR structures of HSPC034 calculated by standard methods that include NMR restraints have improvements in the RMSD to the crystal structure and MR performance in the order DYANA, CYANA, XPLOR-NIH, and CNS with explicit water refinement (CNSw). Further Rosetta refinement of the... - Andrew Perry

Science (New York, N.Y.) (25 June 2009) Communication between organelles is an important feature of all eukaryotic cells. To uncover components involved in mitochondria/endoplasmic reticulum (ER) junctions, we screened for mutants that could be complemented by a synthetic protein designed to artificially tether the two organelles. We identified the Mmm1/Mdm10/Mdm12/Mdm34 complex as a molecular tether between ER and mitochondria. The tethering complex was composed of proteins resident of both ER and mitochondria. Using genome-wide mapping of genetic interactions, we showed that the components of the tethering complex were functionally connected to phospholipid biosynthesis and calcium signaling genes. In mutant cells, phospholipid biosynthesis was impaired. The tethering complex localized to discrete foci, suggesting that discrete sites of close apposition between ER and mitochondria facilitate interorganelle calcium and phospholipid exchange. Benoît Kornmann, Erin Currie, Sean... - Andrew Perry

A very neat way to screen for components involved in organelle-organelle association. I also love the way using a chimeric protein and a complementation screen of mutants becomes "Synthetic Biology". Go buzzwords ! - Andrew Perry

AppRocket replicates a Google App Engine datastore to a MySQL database and vice versa. - Andrew Perry

"Each round you'll be presented with a new spectrum. You have to select the molecule that matches the spectrum." (not sure why I didn't have this bookmarked earlier). - Andrew Perry

CS ROSETTA is a protocol which generates 3D models of proteins, using only the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts as user input. - Andrew Perry