Boitechnology

Sirius is distributed freely from the project website to individuals affiliated with academic and non-profit organizations. Native desktop application installers are available for Windows, Linux and Mac OS X. In addition to providing the downloads, the project site contains Sirius help system, tutorials and screenshots.

Sirius contains a full-featured molecular dynamics (MD) visualization component. It can read output files from AMBER and CHARMM simulations, including compressed and AMBER out files. RMSD changes along the trajectory can be calculated using user-defined atom subsets and displayed in an interactively updated graph. In order to reduce memory requirements, large multifile simulations may be loaded in a buffered mode. If a simulation involves changes in protein fold, Sirius can be set to track and recompute displayed secondary structure features in real time, which provides a convenient way to observe transformations of the structure. The full trajectory or selected frames can be exported as QuickTime video or a set of POV-Ray scene snapshots that can later be converted to a high quality movie.

Sirius features a command line interpreter that can be used to quickly manipulate structure appearance and orientation. The set of commands has been patterned after RasMol, so it’s fully compatible with existing scripts. Additional commands introduced in Sirius have been added to provide support for manipulation of multiple structures loaded at the same time, and to enable more flexible selection.

Existing RasMol scripts can be imported and run within Sirius to produce high quality representations of encoded molecular scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly. Any manually entered commands, however, are executed according to the Sirius coordinate system. For details, refer to Sirius help.

Sirius supports a number of predefined atom/residue sets and color schemes, as well as allows for editing of scripts using the Command Panel interface. In addition, logical operators and parentheses can be used to create complex selection commands.

Sirius supports a variety of applications with a set of features that include
Building and editing chemical structures using a library of fragments
Protein structure and sequence alignment
Command line interpreter and scripting support fully compatible with existing RasMol scripts
Full support for molecular dynamics trajectory visualization
BLAST search directly in Protein Data Bank and Uniprot databases
Ability to move parts of the loaded data while freezing the rest
Interactive calculation of hydrogen bonding, steric clashes, Ramachandran plots
Support for all major structure and sequence formats
Bundled POV-Ray for creating photorealistic images
Integrated selection and coloring across individual visualization components

Sirius is based on molecular graphics code and data structures developed as a part of Molecular Biology Toolkit.

Sirius is a molecular modeling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small molecules and proteins. In addition to high quality interactive 3D graphics, Sirius supports structure building, displaying protein or DNA primary sequences, access to remote data sources and visualization of molecular dynamics trajectories. Sirius can be used for scientific visualization and analysis, as well as for chemistry and biology instruction.

On UNIX platforms Rasmol can communicate with other programs via Tcl/Tk. Under Microsoft Windows, Dynamic Data Exchange (DDE) is used.
multiple alignment program. The responsible Java class can be freely used in other applications.

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.

Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.

RasMol has a complex version history. Starting with the series of 2.7 versions, RasMol is licensed under a dual license (GPL or custom license RASLIC[1]). Thus, RasMol is (along with Molekel, Jmol and PyMOL), among the few open source molecular visualization programs available.

RasMol includes a language (for selecting certain protein chains, or changing colors etc). Jmol has incorporated the RasMol scripting language into its commands.

Protein Databank (PDB) files can be downloaded for visualization from the Research Collaboratory for Structural Bioinformatics (RCSB) bank. These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography or NMR spectroscopy.

CASP, Critical Assessment of Techniques for Protein Structure Prediction, is a biennial experiment sponsored by NIH. CASP represents the Olympic Games of the protein structure prediction community and was established in 1994.

RAPTOR first appeared in CAFASP3 (CASP5) in 2002 and was ranked number one in the individual server group for that year. Since then, RAPTOR has actively participated in every CASP for evaluation purpose and been consistently ranked in the top tier.

The most recent CASP8 ran from May 2008 until August 2008. More than 80 prediction servers and more than 100 human expert groups worldwide registered for the event, where participants attempt to predict the 3D structure from a protein sequence. According to the ranking from Zhang’s group, RAPTOR ranked 2nd among all the servers (meta server and individual servers). Baker lab’s ROBETTA is placed 5th in the same ranking list.

There are many different structure viewers. In RAPTOR, Jmol is used as the structure viewer for examining the generated prediction.

To make it a comprehensive tool set, PSI-BLAST is also included in RAPTOR to let people do homology modeling. People can set up all the necessary parameters by themselves. There are two steps involved in running PSI-BLAST. The first step is to generate the sequence profile. For this step, NR non-redundant database is used. The next step is to let PSI-BLAST search the target sequence against the sequences from the Protein Data Bank. Users can also specify their own database for each step.