Glossary
Scientific and technical terms explained.
A
Ab Initio — 'from the beginning'. Used in computational science to indicate calculations that require no experimental data and only the most basic facts about the system, for example its chemical composition.
Accelrys — the leading computational science company, delivers computational science software that analyzes and solves key research problems, and informatics tools that assist the management and mining of scientific data. The Materials Studio® product family is the leading nanotechnology software package. The Nanotechnology Consortium provides a project framework and a detailed scientific proposal that addresses the challenges of rational nanomaterials and nanodevice design.
ADME/Tox (Absorption, Distribution, Metabolism and Excretion / Toxicity) — the set of properties related to behavior in the body that are critical to the success of a potential drug. They often cause failures in clinical trials, even where the drug has a desired therapeutic effect.
Amorphous Material — solid materials or liquids where there is no order in the structure. Modeling these systems requires the application of advanced statistical techniques or the use of sophisticated approximations. Examples include many polymer systems.
Analytical Instruments — machines used to measure and analyze the structure or properties of chemicals, biological systems, or materials. They often work by measuring the way in which the sample interacts with radiation: X-rays, infrared, ultra-violet, or light. Software can be vital in interpreting results.
Atom — a particle, made up of a nucleus and one or more orbiting electrons, which is the basic unit of a chemical element.
Atomistic Simulation — modeling methods that use the atom as their basic 'building block'. See also molecular modeling.
B
Bioinformatics — the management and analysis of data that describes genes, proteins, and DNA. These are the data types fundamental to biological and genetic research, for example that around the Human Genome Project.
Bond — a chemical connection between two atoms made by the sharing of electrons.
C
CAN — Computer-aided Nanotechnology - see below.
C++ — a programming language, typically used to write large-scale applications, and used in many computational science products.
Catalysis — the process by which catalysts function.
Catalyst — a compound that changes the rate of a chemical reaction without participating in the reaction. Catalysts usually speed a reaction up or allow it to take place at a lower temperature. They are extremely important in chemical and petrochemical processes and in environmental applications, such as cleaning up the exhaust from a car.
Cheminformatics — the management and analysis of data that describes chemical compounds, for example, chemical structure and properties.
Client — the computer through which a user operates software. Calculations requiring more computer power may be transferred to a larger computer known as a server. This is known as client / server computing.
Combinatorial Chemistry — the generation of large collections, or "libraries," of molecules by synthesizing all possible combinations of a set of smaller chemical structures. Usually for automated testing (see High throughput screening).
Computer-aided Nanodesign (CAN) — the use of computer software, usually modeling, simulation, and informatics, to further nanotechnology research and development, building bridges between chemistry and engineering workflow.
Consortium — an approach to nurturing new technologies, in which research organizations join together to part-fund and guide the development of novel software tools for a specific research area. Consortium members validate and apply the software, gaining early access to it.
Crystallography — the determination and characterization of the structure of crystalline materials (see crystals), typically through the use of analytical instruments. Two key types are macromolecular crystallography, which crystallizes proteins to discover their structure, and "small molecule" crystallography, which focuses on materials like drugs and pigments.
Crystals — solid materials consisting of a regularly-repeated unit. They are a vital class of materials, with examples including drugs, pigments, catalysts, minerals, metals, and alloys. Crystals are very amenable to accurate modeling, since calculations based on the fundamental unit can be extrapolated to the whole system.
Crystal Structure — the exact arrangement of molecules or atoms in a crystal. The structure controls vital properties, like strength, stability, color, bioavailability…
D
Distributed Computing — describes the situation where computing tasks are spread over more than one connected computer. For example, the Internet, or client / server computing.
DNA — the basic building-block of life. Each strand of DNA is a made up of chemical units called nucleotides. Strands are twisted into a double-helix shape. Each nucleotide consists of a sugar, a phosphate, and one of four nitrogen-containing fragments called bases. The order of bases is the DNA sequence. This sequence contains the genetic instructions required to create a particular organism (see genes).
Drug Development — the process that works out how to deliver a drug, for example as a pill, spray, or patch.
Drug Discovery — the process of identifying molecules that have a therapeutic effect against a target disease.
E
Electron — a sub-atomic particle. The arrangement of electrons in atoms, molecules, and materials determines much of their chemistry. (See also Quantum Mechanical methods).
Electronic Structure — the arrangement of electrons in a molecule or material. Particularly important in studying chemical reactions, where electron behavior is critical to the making and breaking of chemical bonds, and in solid state materials, such as semiconductors or heterogeneous catalysts, where electrons are shared across the atoms in the structure and their organization controls critical properties like conductivity and reactivity.
F
Force Field — the mathematical approximation used to calculate a molecule or material's energy in molecular mechanics.
Formulation — a product that is a mixture of other chemical components using carefully defined proportions and processes. Examples include some drugs, many foods, cosmetics, and paints.
FORTRAN — a programming language used to write many scientific applications.
G
Grid Computing — splits complex computing tasks into many small components that are run over a 'grid'of networked computers, before being recombined to generate a result. This enables, for example, all of the personal computers in a company to be 'added together' during their idle time to act like a single, much more powerful, computer.
H
High Throughput Screening (HTS) / High Throughput Experimentation (HTE) — the automated trial-and-error testing, using robotics, of very large sets of chemical or materials.
Homology Modeling — methods to determine the structure of a protein based on comparing proteins with similar sequences.
I
In Silico — meaning 'in silicon'. A buzzword to describe research on a computer. Derived from the phrases in vitro ('in glass'- meaning test tube research) and in vivo ('in life'- meaning live animal research), which are commonly used in chemistry.
Informatics — the management and analysis of (usually scientific) data.
J
J2EE — (Java 2 Platform Enterprise Edition) a Java platform designed to simplify application development in complex distributed environments, principally by creating standardized, reusable, modular components.
Java — a programming language, based on C++, and used for writing applications in distributed environments such as the Internet.
K
L
Life Sciences — the complete set of scientific disciplines focused on understanding and intervening in biological systems. Key focuses are discovery of drugs and other therapeutics, and the study of agrochemicals.
Linux — a Unix-like operating system designed to provide personal computer users a free or very low-cost operating system comparable to traditional Unix systems.
M
Macromolecules — large molecules! Usually refers to the complicated molecules that are the basic units of biological systems - proteins and DNA.
Materials Science — the study of the structure and properties of materials. Used by Accelrys to describe its "non life science" business, which also incorporates elements of chemistry and solid-state physics.
Materials Studio® — next-generation software environment for the materials sciences from Accelrys, offering molecular modeling, QSAR, and matinformatics capabilities. Clients run on personal computers, servers run on UNIX, Linux, and Windows.
Matinformatics — the management and analysis of data relating to materials.
Mesoscale Modeling — models with a basic unit just above the molecular scale. Mesoscale modeling is useful for studying behavior of polymers and soft materials that are important to industries like chemicals, foods, cosmetics, and plastics.
Molecular Dynamics — the computation of the motion of atoms within a molecular system using molecular mechanics. This allows the study of structure and key properties like stability, diffusion, binding between molecules, and vibration.
Molecular Mechanics — a fast and approximate method for computing the structure and behavior of molecules or materials based on a series of assumptions that greatly simplify chemistry, for example, that atoms and the bonds that connect them behave like "balls and springs". The approximations make possible the study of large and complex systems, or the very rapid study of smaller systems, not possible with more accurate quantum mechanical methods.
Molecular Modeling — the representation of molecules and materials using 3D computer graphics models. Typically shows the atoms within the material as "balls" and identifies the bonds between them. Usually accompanied by molecular mechanics methods to predict structure and behavior.
Molecular Simulations Inc. — molecular modeling software company. Originated as Biodesign in 1984 and acquired or merged with Biosym, Polygen, BioCAD, and Cambridge Molecular Design, Oxford Molecular, Synopsys, and Synomics to create Accelrys.
Molecule — the basic unit of any substance; consists of atoms connected by bonds.
Monte Carlo Simulation — simulation methods that use random numbers to generate possible molecules or materials and then identify the optimal system, for example through molecular mechanics.
N
Nanomaterials by Design — the use of computation to design materials with desired properties - see also Rational Nanotechnology Design.
Nanotechnology — the study of systems and devices on the molecular scale. Nanotechnology problems are very amenable to molecular modeling, and a huge growth area in global R&D.
Nanotechnology Consortium — launched in 2004 by Accelrys, the Nanotechnology Consortium is a group of industrial researchers, academic experts, and Accelrys scientists, focused on developing, validating, and applying molecular simulation to a particular research area. Its goal is to extend existing and create new software tools, which enable the rational design of nanomaterials and nanodevices.
.NET — Microsoft's collection of supporting technology for programming web services (applications that use the Web rather than your own computer for various underlying tasks).
O
Oracle® — the industry-standard relational database.
P
Pharmacophore — a set of characteristics common to a series of known active molecules that can be represented graphically and used to find other possible active molecules.
Platform — an underlying computer system on which software applications can run. May refer to a particular brand or type of hardware or to a software system the provides the services for other applications.
Polymer — long-chain molecules consisting of repeating chemical units called monomers. Polymeric materials include plastics and rubber.
Polymorphism — the ability of one molecule to crystallize into more than one crystal structure. Can affect important properties like stability, color, and dosages in drugs.
Protein — the basic structural components of cells and tissues and of the enzymes controlling biochemical reactions. Proteins are complex macromolecules made up of long chains of subunits called amino acids. These chains fold into complex three-dimensional shapes. Protein modeling using methods like homology modeling and molecular dynamics is a central technology in drug discovery, usually aiming to identify targets for potential drugs.
Proteomics — the effort to establish the identities, quantities, structures and biochemical and cellular functions of all proteins in an organism.
Q
QSAR — Quantitative Structure-Activity Relationship. A statistical relationship, derived from experimental data, between a property of interest and key structural characteristics of the molecules in the study - like their shape.
Quantum Mechanical (QM) Methods — very accurate calculations of chemical structure and behavior based on solving the Schrödinger equation, the fundamental equation of chemistry. QM methods describe molecules and materials using electrons as their basic unit and allow property prediction, the study of reactions, and the understanding of electronic structure.
R
Rational Nanotechnology Design — the use of computation in the nanotechnology part of a manufacturing process to refine the number and potential of materials with desired properties. See also Nanomaterials by Design.
Reaction — the process by which two or more molecules combine and rearrange to form a new molecule or series of molecules. Reactions are the basis of most chemical processes and understanding them the essence of much of chemistry. Reactions usually involve the making and breaking of bonds, thus their accurate modeling requires quantum mechanical methods.
S
Sequence — the order of bases in DNA or of amino acids in a protein. Usually, each unit in the sequence is represented by a single letter. Bioinformatics, genomics, and proteomics methods analyze these sequences, for example to try to relate them to the function of the protein or DNA.
Server — a computer or piece of software used to perform (usually demanding) computational tasks, such as complicated calculations or storage of large databases. A server is shared across a network, and accessed via another computer -- see Client.
Simulation— the use of a computer to imitate the behavior of a real system, leading to a better understanding of that system. Molecular simulation applies and combines methods and strategies like molecular modeling, molecular mechanics, QM, and mesoscale modeling to study chemical systems.
Solid State Materials — any solid, but typically used to mean materials like semiconductors, non-linear optical materials, metal oxides, glasses, and ceramics. These are critical to technologically significant problems in industries including chemicals, petrochemicals electronics, and aerospace.
T
Target — used in drug discovery to mean a region of a protein that is believed to be open to intervention by a drug, usually by the drug molecule binding to the target site and changing its behavior.
U
UNIX — a computer operating system widely used on the powerful graphics workstations that were the basic system for the molecular modeling market in the 1980s and 1990s.
V
Visual Basic (VB) — a programming environment from Microsoft in which a programmer uses a graphical user interface to choose, modify, and assemble sections of code written in the BASIC programming language.
W
Windows® — the Microsoft operating system for personal computers
XYZ