PyMOLPyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrodinger, LLC.
Molecular graphicsMolecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically.
OpenGLOpenGL (Open Graphics Library) is a cross-language, cross-platform application programming interface (API) for rendering 2D and 3D vector graphics. The API is typically used to interact with a graphics processing unit (GPU), to achieve hardware-accelerated rendering. Silicon Graphics, Inc. (SGI) began developing OpenGL in 1991 and released it on June 30, 1992; applications use it extensively in the fields of computer-aided design (CAD), virtual reality, scientific visualization, information visualization, flight simulation, and video games.
IntelIntel Corporation (commonly known as Intel) is an American multinational corporation and technology company headquartered in Santa Clara, California. It is one of the world's largest semiconductor chip manufacturer by revenue, and is one of the developers of the x86 series of instruction sets found in most personal computers (PCs). Incorporated in Delaware, Intel ranked No. 45 in the 2020 Fortune 500 list of the largest United States corporations by total revenue for nearly a decade, from 2007 to 2016 fiscal years.
CPU cacheA CPU cache is a hardware cache used by the central processing unit (CPU) of a computer to reduce the average cost (time or energy) to access data from the main memory. A cache is a smaller, faster memory, located closer to a processor core, which stores copies of the data from frequently used main memory locations. Most CPUs have a hierarchy of multiple cache levels (L1, L2, often L3, and rarely even L4), with different instruction-specific and data-specific caches at level 1.
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
ARM architecture familyARM (stylised in lowercase as arm, formerly an acronym for Advanced RISC Machines and originally Acorn RISC Machine) is a family of reduced instruction set computer (RISC) instruction set architectures for computer processors, configured for various environments. Arm Ltd. develops the architectures and licenses them to other companies, who design their own products that implement one or more of those architectures, including system on a chip (SoC) and system on module (SOM) designs, that incorporate different components such as memory, interfaces, and radios.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
Intel 4004The Intel 4004 is a 4-bit central processing unit (CPU) released by Intel Corporation in 1971. Sold for US60(,449.43 in 2023), it was the first commercially produced microprocessor, and the first in a long line of Intel CPUs. The 4004 was the first significant example of large scale integration, showcasing the superiority of the MOS silicon gate technology (SGT). Compared to the incumbent technology, the SGT integrated on the same chip area twice the number of transistors with five times the operating speed. Protein Data BankThe 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.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
ProteinProteins 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, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Protein quaternary structureProtein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.
Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are 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 folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
Meltdown (security vulnerability)Meltdown is one of the two original transient execution CPU vulnerabilities (the other being Spectre). Meltdown affects Intel x86 microprocessors, IBM POWER processors, and some ARM-based microprocessors. It allows a rogue process to read all memory, even when it is not authorized to do so. Meltdown affects a wide range of systems. At the time of disclosure (2018), this included all devices running any but the most recent and patched versions of iOS, Linux, macOS, or Windows.
Intel Graphics TechnologyIntel Graphics Technology (GT) is the collective name for a series of integrated graphics processors (IGPs) produced by Intel that are manufactured on the same package or die as the central processing unit (CPU). It was first introduced in 2010 as Intel HD Graphics and renamed in 2017 as Intel UHD Graphics. Intel Iris Graphics and Intel Iris Pro Graphics are the IGP series introduced in 2013 with some models of Haswell processors as the high-performance versions of HD Graphics.
Protein primary structureProtein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequencess.
Computer mouseA computer mouse (plural mice, also mouses) is a hand-held pointing device that detects two-dimensional motion relative to a surface. This motion is typically translated into the motion of the pointer (called a cursor) on a display, which allows a smooth control of the graphical user interface of a computer. The first public demonstration of a mouse controlling a computer system was in 1968. Mice originally used two separate wheels to directly track movement across a surface: one in the X-dimension and one in the Y.
OpenGL ESOpenGL for Embedded Systems (OpenGL ES or GLES) is a subset of the OpenGL computer graphics rendering application programming interface (API) for rendering 2D and 3D computer graphics such as those used by video games, typically hardware-accelerated using a graphics processing unit (GPU). It is designed for embedded systems like smartphones, tablet computers, video game consoles and PDAs. OpenGL ES is the "most widely deployed 3D graphics API in history". The API is cross-language and multi-platform.
Amino acidAmino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the α-amino acids, from which proteins are composed. Only 22 α-amino acids appear in the genetic code of all life. Amino acids can be classified according to the locations of the core structural functional groups, as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, ionization, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.
