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Downloads and Upgrades: Oct 29, 2010

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This week, Tripos released Sybyl-X Version 1.2.

The latest release of the molecular modeling suite focuses on streamlined workflows for life science researchers and includes a new, project-oriented interface for quantitative structure-activity relationship studies.

Additionally, the developers have added Surflex-Dock's fragment-constrained docking and treatment of protein flexibility, which the company said will allow scientists to more closely approximate real-world conditions and to use known information about particular fragment placements to guide docking.


The National Center for Biotechnology Information has launched Images, a database of more than 2.5 million images and figures from medical and life sciences journals.

According to the developers, Images will have a wide range of uses for a variety of groups such as clinicians looking for visual representations of a disease or condition, researchers searching for studies with certain types of analyses, students seeking diagrams that elucidate complex processes such as DNA replication, professionals or educators looking for images for presentations, and patients wanting to better understand disease.

The database lets users search images based on keywords and other parameters, such as author and publication date, and save them. Users can also share saved images and data with others through the My NCBI feature, which allows users to customize their search and display preferences, and build bibliographies, among other functions.

The resource currently contains images and figures contained in NCBI's PubMed Central full-text digital archive of biomedical and life sciences journal literature and may be expanded to include other NCBI resources, such as the Bookshelf database of biomedical books and reports.


SoftGenetics has released an updated version of its genotyping software, GeneMarker.

The developers said that the latest version of the software includes a new module for comparative analysis of cystic fibrosis types for use with Gen-Probe’s Elucigene CF kit as well as visualization of mutant alleles generated by the Abbott Cystic Fibrosis Genotyping assay. The new release also includes a user-management tool that controls access rights and provides an analysis audit trail.

Other new features include a macromolecules analysis module for analyzing carbohydrates, polysaccharides, proteins and polypeptides, without the use of an internal size standard; and two new sizing algorithms that allow for linear sizing of DNA fragments from 20 bp to more than 1000 bp, as well as the sizing of nonlinear data.

The Scan

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.

Sequencing Study Leads to Vaccine Target in Bacteria Behind Neonatal Meningitis

Researchers eBioMedicine track down potential vaccine targets with transposon sequencing on mutant bacteria causing neonatal meningitis in mouse models of the disease.

Multiple Myeloma Progression Influenced by Immune Microenvironment Expression

Researchers in NPJ Genomic Medicine compare RNA sequencing profiles of 102,207 individual cells in bone marrow samples from 18 individuals with rapid or non-progressing multiple myeloma.

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.