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Glossary
All the scientific and technical terms explained.
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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 recently (2004)
launched Nanotechnology Consortium provides a project
framework and a detailed scientific proposal that addresses
the challenges of rational nanomaterials and nanodevice design.
More >>
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. More
>>
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.
More
>>
.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
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