The program allows fully automated application of the method. of G-Protein Coupled Receptor alpha1A. Additionally, a large-scale evaluation using the DUD (directory site of useful decoys) dataset was performed. DUD contains 2950 active ligands for 40 different receptors, with 36 decoy compounds for each active ligand. PharmaGist enrichment rates are comparable with other state-of-the-art tools for virtual screening. Availability The software is usually available for download. A user-friendly web interface for pharmacophore detection is usually available at http://bioinfo3d.cs.tau.ac.il/PharmaGist. Introduction Virtual Screening (VS) is usually a computational approach to drug discovery that successfully complements High Throughput Screening (HTS) for hit detection.1 The objective is to use a computational approach for quick cost-effective evaluation of large virtual databases of chemical compounds in order to identify a set of candidates to be synthesized and examined experimentally for their biological activity. Unlike HTS, virtual screening is not based on a brute-force search, but on some starting information around the receptor under inspection or on its active ligands. Virtual screening methods can be divided into two broad groups: structure-based and ligand-based. In case the three-dimensional (3D) structure of the target receptor or of its binding site is usually available, docking is usually a highly effective technique for virtual screening.2,3 In the absence of structural information around the receptor, virtual screening methods are mainly based on structural similarity between known and potential active ligands. The rationale is usually that molecules that share some structural similarity may have a similar activity. Some methods make use of a known active ligand as a query to extract structurally similar compounds from large databases.4 Among these are the FlexS5,6 and fFlash7 methods. These methods perform a 3D structural alignment between a pair of compounds, a query ligand assumed to be rigid and each database compound treated as flexible. When a set of active ligands is usually available, it is possible to compute their shared pharmacophore. A is usually defined as the 3D arrangement of features that is crucial for any ligand molecule in order to interact with a target receptor in a specific binding site. Once recognized, a pharmacophore can serve as an important model for virtual screening, especially in case where the 3D structure of the receptor is usually unknown and docking techniques are not relevant. The strength of pharmacophore-based screening compared to other ligand similarity screening approaches lies in the ability to detect a diverse set CUDC-305 (DEBIO-0932 ) of putative active compounds with totally different chemical scaffolds. This increases the chances that some of the detected compounds will pass all the stages of drug development. Besides screening, pharmacophore is usually a powerful model also in other applications of drug development, like design, lead optimization, ADME/Tox studies and CUDC-305 (DEBIO-0932 ) Chemogenomics.8,9 Many methods are available for identifying pharmacophore models from a set of ligands that have been observed CUDC-305 (DEBIO-0932 ) to interact with the same receptor.10C12 Generally, these methods search for the largest 3D pattern of CUDC-305 (DEBIO-0932 ) features responsible for binding that is shared by all or most input ligands. From your computational standpoint, this task is usually challenging with respect to both the quantity of input ligands and their flexibility. The various methods mainly differ in three aspects: (i) the chosen feature descriptors and structure representation, Mouse monoclonal antibody to HAUSP / USP7. Ubiquitinating enzymes (UBEs) catalyze protein ubiquitination, a reversible process counteredby deubiquitinating enzyme (DUB) action. Five DUB subfamilies are recognized, including theUSP, UCH, OTU, MJD and JAMM enzymes. Herpesvirus-associated ubiquitin-specific protease(HAUSP, USP7) is an important deubiquitinase belonging to USP subfamily. A key HAUSPfunction is to bind and deubiquitinate the p53 transcription factor and an associated regulatorprotein Mdm2, thereby stabilizing both proteins. In addition to regulating essential components ofthe p53 pathway, HAUSP also modifies other ubiquitinylated proteins such as members of theFoxO family of forkhead transcription factors and the mitotic stress checkpoint protein CHFR (ii) the technique for addressing the flexibility of the ligands, and (iii) the definition of the searched common pattern and the algorithm employed for identifying it.10,13 All ligand-based methods for pharmacophore detection represent the input ligands by their CUDC-305 (DEBIO-0932 ) features. The selection of feature descriptions is mainly based on the desired level of.