No abstract

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.

Despite intense interest in expanding chemical space, libraries of hundreds-of-millions to billions of diverse molecules have remained inaccessible. Here, we investigate structure-based docking of 170 million make-on-demand compounds from 130 well-characterized reactions. The resulting library is diverse, representing over 10.7 million scaffolds otherwise unavailable. The library was docked against AmpC β-lactamase and the D 4 dopamine receptor. From the top-ranking molecules, 44 and 549 were synthesized and tested, respectively. This revealed an unprecedented phenolate inhibitor of AmpC, which was optimized to 77 nM, the most potent non-covalent AmpC inhibitor known. Crystal structures of this and other new AmpC inhibitors confirmed the docking predictions. Against D 4 , hit rates fell monotonically with docking score, and a hit-rate vs. score curve predicted 453,000 D 4 ligands in the library. Of 81 new chemotypes discovered, 30 were sub-micromolar, including a 180 pM sub-type selective agonist.