Digital Briefs

Software

(1) AKS² (almaknowledgeserver 2) is a management software system that analyzes and organizes biochemical and biomedical literature. The system makes automated text analytics of Medline abstracts simple even for the casual user. AKS² extracts biochemical or biomedical keywords and phrases from the abstracts, analyzes all the relationships between those key concepts on a daily basis, and presents the results in a summary report. One can visualize and explore the concepts that are related in the literature with an interactive graphical tool. AKS² also integrates data from the most relevant sources, thus enabling one to extract all the information about a certain topic from external databases. Literature search findings can be stored and shared within the system or reports can be generated in PDF format. Active Motif, www.activemotif.com

(2) FlexX Release 2.1 is the latest edition of the FlexX protein-ligand docking tool. FlexX 2.1 now supports large input library files and can be accessed from the molecular modeling environments of SYBYL and MOE. FlexX-Screen is a new module for rapidly screening vast corporate compound libraries at less than 1 second per compound with no loss in accuracy compared with standard FlexX. In addition, the module also contains many different customizable filters for toxicity, reactivity, and druglikeness. The software is supported on Windows, Sun, Irix SGI, and Linux. BioSolveIT, www.biosolveit.com

(3) Molecule Evoluator 4.0 is a Windows application that generates novel molecular structures using evolutionary search algorithm principles and interactive searches. Physicochemical properties, including solubility, are calculated on the fly and are used to filter and sort the generated molecules. In the latest version of the software, chemical feasibility is enhanced by introducing fragment-based scaffold generation and common ring systems. Substructures can be fixed to serve as the input for a new set of derivatives. Structures are easily edited and can be imported from and exported to other software packages. Cidrux, www.cidrux.com

Databases

Generated Database of Chemical Universe of Small Molecules is a database that covers every possible organic molecule of C, N, O, or F up to 11 atoms and that is constructed under constraints that define chemical stability and synthetic feasibility. The database contains 26.4 million compounds, the vast majority of which have never been synthesized. Searching through this database may allow researchers to identify new synthetic targets with interesting properties. Though an earlier version of this database has been reported, this version includes molecules with small rings and triple bonds. www.dcb.unibe.ch/groups/reymond/

Chemkey Search is a database of 110,000 references from all the major organic chemistry journals. Particular attention has been devoted to such topics as synthetic methodology, asymmetric synthesis, natural product synthesis, heterocyclic chemistry, reactive intermediates, organometallic chemistry, and stereochemistry. Searching generally takes fewer than 15 seconds, and the display is instantaneous. Key references are provided, which enable the user to peruse the literature for additional references. The database allows the user to conduct both wide and narrow searching through wildcard and Boolean logic. Yearly updates contain 5,000 new references. The software is available for both the Mac and PC. Heterodata, euch6f.chem.emory.edu/index.html

Online

(4) Techquisition is a new online community for buyers and sellers of technology whose goal is to facilitate the technology-transfer process in an efficient and effective manner. Techquisition is free to both buyers and sellers of technology, allowing them to search for each other according to the industries they specify in their user settings. The site contains two separate databases that can be queried independently by either potential licensors or licensees. In addition, the users of Techquisition.com have flexible control over the information conveyed and to whom that information is conveyed. Techquisition, www.techquisition.com