Chemical spaceChemical space is a concept in cheminformatics referring to the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. It contains millions of compounds which are readily accessible and available to researchers. It is a library used in the method of molecular docking. A chemical space often referred to in cheminformatics is that of potential pharmacologically active molecules. Its size is estimated to be in the order of 1060 molecules.
Biological activityIn pharmacology, biological activity or pharmacological activity describes the beneficial or adverse effects of a drug on living matter. When a drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other constituents. Among the various properties of chemical compounds, pharmacological/biological activity plays a crucial role since it suggests uses of the compounds in the medical applications.
Java (software platform)Java is a set of computer software and specifications developed by James Gosling at Sun Microsystems that provides a system for developing application software and deploying it in a cross-platform computing environment. Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. Java applets, which are less common than standalone Java applications, were commonly run in secure, sandboxed environments to provide many features of native applications through being embedded in HTML pages.
Small moleculeIn molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; the terms are equivalent in the literature. Larger structures such as nucleic acids and proteins, and many polysaccharides are not small molecules, although their constituent monomers (ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively) are often considered small molecules.
Java Platform, Standard EditionJava Platform, Standard Edition (Java SE) is a computing platform for development and deployment of portable code for desktop and server environments. Java SE was formerly known as Java 2 Platform, Standard Edition (J2SE). The platform uses Java programming language and is part of the Java software-platform family. Java SE defines a range of general-purpose APIs—such as Java APIs for the Java Class Library—and also includes the Java Language Specification and the Java Virtual Machine Specification.
Drug discoveryIn the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate medications are discovered. Historically, drugs were discovered by identifying the active ingredient from traditional remedies or by serendipitous discovery, as with penicillin. More recently, chemical libraries of synthetic small molecules, natural products or extracts were screened in intact cells or whole organisms to identify substances that had a desirable therapeutic effect in a process known as classical pharmacology.
Java Web StartIn computing, Java Web Start (also known as JavaWS, javaws or JAWS) is a deprecated framework developed by Sun Microsystems (now Oracle) that allows users to start application software for the Java Platform directly from the Internet using a web browser. The technology enables seamless version updating for globally distributed applications and greater control of memory allocation to the Java virtual machine. Java Web Start was distributed as part of the Java Platform until being removed in Java SE 11, following its deprecation in Java SE 9.
Java virtual machineA Java virtual machine (JVM) is a virtual machine that enables a computer to run Java programs as well as programs written in other languages that are also compiled to Java bytecode. The JVM is detailed by a specification that formally describes what is required in a JVM implementation. Having a specification ensures interoperability of Java programs across different implementations so that program authors using the Java Development Kit (JDK) need not worry about idiosyncrasies of the underlying hardware platform.
Structure–activity relationshipThe structure–activity relationship (SAR) is the relationship between the chemical structure of a molecule and its biological activity. This idea was first presented by Crum-Brown and Fraser in 1865. The analysis of SAR enables the determination of the chemical group responsible for evoking a target biological effect in the organism. This allows modification of the effect or the potency of a bioactive compound (typically a drug) by changing its chemical structure.
MacromoleculeA macromolecule is a very large molecule important to biological processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, and carbohydrates) and large non-polymeric molecules such as lipids, nanogels and macrocycles. Synthetic fibers and experimental materials such as carbon nanotubes are also examples of macromolecules.
MoleculeA 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 biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.
Gaseous signaling moleculesGaseous signaling molecules are gaseous molecules that are either synthesized internally (endogenously) in the organism, tissue or cell or are received by the organism, tissue or cell from outside (say, from the atmosphere or hydrosphere, as in the case of oxygen) and that are used to transmit chemical signals which induce certain physiological or biochemical changes in the organism, tissue or cell. The term is applied to, for example, oxygen, carbon dioxide, sulfur dioxide, nitrous oxide, hydrogen cyanide, ammonia, methane, hydrogen, ethylene, etc.
JavaFXJavaFX is a software platform for creating and delivering desktop applications, as well as rich web applications that can run across a wide variety of devices. JavaFX has support for desktop computers and web browsers on Microsoft Windows, Linux (including Raspberry Pi), and macOS, as well as mobile devices running iOS and Android, through Gluon Mobile. With the release of JDK 11 in 2018, Oracle made JavaFX part of the OpenJDK under the OpenJFX project, in order to increase the pace of its development.
Chemical databaseA chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data. Bioactivity databases correlate structures or other chemical information to bioactivity results taken from bioassays in literature, patents, and screening programs. Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D structural formulae).
Chemical bondA chemical bond is a lasting attraction between atoms or ions that enables the formation of molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds, or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force, and hydrogen bonding.
PubChemPubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains multiple substance descriptions and small molecules with fewer than 100 atoms and 1,000 bonds.
DatabaseIn computing, a database is an organized collection of data (also known as a data store) stored and accessed electronically through the use of a database management system. Small databases can be stored on a , while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance.
MapA map is a symbolic depiction emphasizing relationships between elements of some space, such as objects, regions, or themes. Many maps are static, fixed to paper or some other durable medium, while others are dynamic or interactive. Although most commonly used to depict geography, maps may represent any space, real or fictional, without regard to context or scale, such as in brain mapping, DNA mapping, or computer network topology mapping.
Virtual screeningVirtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme. Virtual screening has been defined as "automatically evaluating very large libraries of compounds" using computer programs. As this definition suggests, VS has largely been a numbers game focusing on how the enormous chemical space of over 1060 conceivable compounds can be filtered to a manageable number that can be synthesized, purchased, and tested.
