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Sirius Visualization Software
Sirius is a molecular modelling 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. Sirius supports high quality interactive 3D graphics, structure building, displaying protein or DNA primary sequences, access to remote data sources, and visualizing molecular dynamics trajectories. It can be used for scientific visualization and analysis, and chemistry and biology 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 * Command line interpreter and scripting support fully compatible with extant RasMol scripts * Full support for molecular dynamics trajectory visualizing * BLAST search directly in Protein Data Bank and Uniprot databases * A ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sirius Large
Sirius is the brightest star in the night sky. Its name is derived from the Greek word , or , meaning 'glowing' or 'scorching'. The star is designated α Canis Majoris, Latinized to Alpha Canis Majoris, and abbreviated Alpha CMa or α CMa. With a visual apparent magnitude of −1.46, Sirius is almost twice as bright as Canopus, the next brightest star. Sirius is a binary star consisting of a main-sequence star of spectral type A0 or A1, termed Sirius A, and a faint white dwarf companion of spectral type DA2, termed Sirius B. The distance between the two varies between 8.2 and 31.5 astronomical units as they orbit every 50 years. Sirius appears bright because of its intrinsic luminosity and its proximity to the Solar System. At a distance of , the Sirius system is one of Earth's nearest neighbours. Sirius is gradually moving closer to the Solar System, so it is expected to increase in brightness slightly over the next 60,000 years, reaching a peak magnitude of â ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move, grow, and reproduce. Finally, all organisms are able to regulate their own internal environments. Biologists are able to study life at multiple levels of organization, from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations.Based on definition from: Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. Like other scientists, biologists use the sc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 the square root of the second sample moment of the differences between predicted values and observed values or the quadratic mean of these differences. These deviations are called '' residuals'' when the calculations are performed over the data sample that was used for estimation and are called ''errors'' (or prediction errors) when computed out-of-sample. The RMSD serves to aggregate the magnitudes of the errors in predictions for various data points into a single measure of predictive power. RMSD is a measure of accuracy, to compare forecasting errors of different models for a particular dataset and not between datasets, as it is scale-dependent. RMSD is always non-negative, and a value of 0 (almost never achieved in practice) would ind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia of New Jersey'', Rutgers University Press, . Amber is used in jewelry and has been used as a healing agent in folk medicine. There are five classes of amber, defined on the basis of their chemical constituents. Because it originates as a soft, sticky tree resin, amber sometimes contains animal and plant material as inclusions. Amber occurring in coal seams is also called resinite, and the term ''ambrite'' is applied to that found specifically within New Zealand coal seams. Etymology The English word ''amber'' derives from Arabic (ultimately from Middle Persian ''ambar'') via Middle Latin ''ambar'' and Middle French ''ambre''. The word was adopted in Middle English in the 14th century ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sirius Rasmol Import
Sirius is the brightest star in the night sky. Its name is derived from the Greek word , or , meaning 'glowing' or 'scorching'. The star is designated α Canis Majoris, Latinized to Alpha Canis Majoris, and abbreviated Alpha CMa or α CMa. With a visual apparent magnitude of −1.46, Sirius is almost twice as bright as Canopus, the next brightest star. Sirius is a binary star consisting of a main-sequence star of spectral type A0 or A1, termed Sirius A, and a faint white dwarf companion of spectral type DA2, termed Sirius B. The distance between the two varies between 8.2 and 31.5 astronomical units as they orbit every 50 years. Sirius appears bright because of its intrinsic luminosity and its proximity to the Solar System. At a distance of , the Sirius system is one of Earth's nearest neighbours. Sirius is gradually moving closer to the Solar System, so it is expected to increase in brightness slightly over the next 60,000 years, reaching a peak magnitude of â ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 Aaron A. Collins for Amiga computers. There are also influences from the earlier Polyray raytracer because of contributions from its author, Alexander Enzmann. POV-Ray is free and open-source software, with the source code available under the AGPL-3.0-or-later license. History Sometime in the 1980s, David Kirk Buck downloaded the source code for a Unix ray tracer to his Amiga. He experimented with it for a while and eventually decided to write his own ray tracer named DKBTrace after his initials. He posted it to the "You Can Call Me Ray" bulletin board system (BBS) in Chicago, thinking others might be interested in it. In 1987, Aaron A. Collins downloaded DKBTrace and began working on an x86 port of it. He and David Buck collaborated to add ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles (called φ and φ' by Ramachandran). The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide planar. The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Cα-C) angle in dotted lines. Because dihedral angle values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For ins ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the second-row elements nitrogen (N), oxygen (O), and fluorine (F). Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms and can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Geor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
