Sirius is a

molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scie ...

and analysis system developed at

San Diego Supercomputer Center The San Diego Supercomputer Center (SDSC) is an organized research unit of the University of California, San Diego (UCSD). SDSC is located at the UCSD campus' Eleanor Roosevelt College east end, immediately north the Hopkins Parking Structure ...

. Sirius is designed to support advanced user requirements that go beyond simple display of small

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bio ...

s and

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

s. Sirius supports high quality interactive

3D graphics 3D computer graphics, or “3D graphics,” sometimes called CGI, 3D-CGI or three-dimensional computer graphics are graphics that use a three-dimensional representation of geometric data (often Cartesian) that is stored in the computer for th ...

, structure building, displaying

or DNA

primary sequence Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length sc ...

s, access to remote data sources, and visualizing

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of th ...

trajectories. It can be used for

scientific visualization Scientific visualization ( also spelled scientific visualisation) is an interdisciplinary branch of science concerned with the visualization of scientific phenomena. Michael Friendly (2008)"Milestones in the history of thematic cartography, st ...

and analysis, and chemistry and

biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditar ...

instruction. This software is no longer supported as of 2011.

Key features

Sirius supports a variety of applications with a set of features, including: * Building and editing chemical structures using a library of fragments * Protein structure and

sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Ali ...

* Command line interpreter and scripting support fully compatible with extant

RasMol RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Say ...

scripts * Full support for

trajectory visualizing *

BLAST Blast or The Blast may refer to: *Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), ...

search directly in

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...

and

Uniprot UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

databases * Ability to move parts of the loaded data while freezing the rest * Interactive calculation of

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing ...

ing, steric clashes,

Ramachandran plot In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a �,ψplot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed region ...

s * Support for all major structure and sequence formats * Bundled

POV-Ray The Persistence of Vision Ray Tracer, most commonly acronymed as POV-Ray, is a cross-platform ray-tracing program that generates images from a text-based scene description. It was originally based on DKBTrace, written by David Kirk Buck and Aaro ...

for creating photorealistic images * Integrated selection and coloring across individual visualizing components Sirius is based on molecular graphics code and data structures developed as a part of the Molecular Biology Toolkit.

RasMol-compatible scripting

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

, so it's fully compatible with extant scripts. Added commands introduced in Sirius provide support for manipulating multiple structures loaded at the same time, and enable more flexible selection. Extant 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. Sirius supports several predefined atom-residue sets and color schemes, allows editing of scripts using the Command Panel interface, and logical operators and parentheses can be used to create complex selection commands.

Visualizing molecular dynamics trajectories

Sirius contains a full-featured molecular dynamics visualizing component. It can read output files from

AMBER Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In M ...

and CHARMM simulations, including compressed and AMBER out files.

RMSD The root-mean-square deviation (RMSD) or root-mean-square error (RMSE) is a frequently used measure of the differences between values (sample or population values) predicted by a model or an estimator and the values observed. The RMSD represents ...

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

fold, Sirius can be set to track and recompute displayed

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

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 QuickTime is an extensible multimedia framework developed by Apple Inc., capable of handling various formats of digital video, picture, sound, panoramic images, and interactivity. Created in 1991, the latest Mac version, QuickTime X, is a ...

video or a set of

scene snapshots that can later be converted to a high quality movie.

Access and download

Sirius is distributed freely from the project website to individuals affiliated with academic and non-profit organizations.Sirius downloads
/ref> Native desktop application installers are available for

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for ...

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which i ...

, and

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of ...

References

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External links