On the creation of thermal equations of state for use in Dioptas

Dioptas is a widely used software package for integrating and analysing 2-dimensional diffraction images. To help interpret the integrated diffraction profiles it produces, Dioptas users can input files that parameterise a material's thermal equation of state (EoS), enabling the positions of the Bragg peaks from that material to be calculated as a function of pressure and temperature. However, care is needed to ensure that these input files correctly describe the thermal EoS of interest. Here we describe the thermal EoS model used by Dioptas and show how existing thermal EoS should be reparameterised so as to be used correctly in Dioptas. Input EoS files suitable for use with Dioptas are provided for the following commonly-used pressure calibrants and pressure transmitting media: Al, Au, Cu, Mo, Nb, Pt, Ta, hcp-Fe, MgO, NaCl-B1, NaCl-B2, KCl-B2, and Ne.</p

TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe