Abstract Summary: Allostery allows for the fine-tuning of protein function. Targeting allosteric sites is gaining increasing recognition as a novel strategy in drug design. The key challenge in the discovery of allosteric sites has strongly motivated the development of computational methods and thus high-quality, publicly accessible standard data have become indispensable. Here, we report benchmarking data for experimentally determined allosteric sites through a complex process, including a ‘Core set’ with 235 unique allosteric sites and a ‘Core-Diversity set’ with 147 structurally diverse allosteric sites. These benchmarking sets can be exploited to develop efficient computational methods to predict unknown allosteric sites in proteins and reveal unique allosteric ligand–protein interactions to guide allosteric drug design. Availability and implementation: The benchmarking sets are freely available at http://mdl.shsmu.edu.cn/asbench. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

MOTIVATION: The use of allosteric modulators as preferred therapeutic agents against classic orthosteric ligands has colossal advantages, including higher specificity, fewer side effects and lower toxicity. Therefore, the computational prediction of allosteric sites in proteins is receiving increased attention in the field of drug discovery. Allosite is a newly developed automatic tool for the prediction of allosteric sites in proteins of interest and is now available through a web server. AVAILABILITY: The Allosite server and tutorials are freely available at http://mdl.shsmu.edu.cn/AST CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: ODORactor is an open access web server aimed at providing a platform for identifying odorant receptors (ORs) for small molecules and for browsing existing OR-ligand pairs. It enables the prediction of ORs from the molecular structures of arbitrary chemicals by integrating two individual functionalities: odorant verification and OR recognition. The prediction of the ORs for several odorants was experimentally validated in the study. In addition, ODORactor features a comprehensive repertoire of olfactory information that has been manually curated from literature. Therefore, ODORactor may provide an effective way to decipher olfactory coding and could be a useful server tool for both basic olfaction research in academia and for odorant discovery in industry. AVAILABILITY: Freely available at http://mdl.shsmu.edu.cn/ODORactor CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Web Services Security describes enhancements to SOAP messaging to provide quality of protection through message integrity, message confidentiality, and single message authentication. In this paper, we propose an implementation based on proxy mechanism. We devise an architecture that provides authentication based on PKI and authorization based on PMI to Web Service with least influence of the original codes to call Web Service. We also provide configuration interface for users to change their default security policy. Our system is independent of any web service server and independent of any programming language. You can you it without or just a bit of modification to your source codes.