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Acca
In the context of molecular modelling or chemical
informatics, Acca is a program which assists in conformation searching,
by transferring information between related conformation searches.
ACID
In the context of databases, ACID stands for Atomic,
Consistent, Isolated and Durable. The ACID test for a database
transaction requires: (i) Atomic - a transaction either succeeds
completely, or fails completely, so the database is not left in a
half-updated state. (ii) Consistent - a transaction always leaves the
database in a correct state. (iii) Isolated - executing transactions do
not affect other transactions (iv) Durable - the data should survive
ADME
ADME stands for Absorption, Distribution, Metabolism and
Excretion. These four aspects of a drug's action are all important.
AM1
Austin Model 1. A semi empirical molecular orbital method
AMBER
A molecular mechanics force field
API
Application Program Interface: many computer programs
(including operating system) are designed so that other programs can
access some of their functionality. The specification of how to do this
is the API.
ASP
Application Service Provider: Applications can be delivered
over the internet as well as data. Is this the future? Many companies
are looking into this evolving delivery model. More information is
available from the ASP
Industry Consortium. (October 2000)
ASP
Active Server Pages: a web page which contains a script to be
which works out what information to send to the user. Typically it is
used to process a request for some information from a database. For
more information see the
ASP toolbox or LearnASP
(September 2001)
Block Diagonal Newton Raphson. A minimisation algorithm
BFGS
Broyden-Fletcher-Goldfarb-Shanno. A minimisation algorithm
BLAST
Basic Local Alignment Search Tool: a set of similarity search
programs for DNA and protein sequences, originally published in the
Journal of Molecular Biology (1990, 215(3):403-10 Altschul SF, Gish W,
Miller W, Myers EW, Lipman DJ). Several web resources are available
including the NCBI
- NIH and Washington
University.
BLYP
A functional for density functional calculations
BRENDA
A collection of enzyme functional data
CADPAC
Cambridge Analytical Derivatives Package. An ab
initio molecular orbital theory package
CAOS
Computer-Aided Organic Synthesis
CAS
Chemical Abstracts Service. An organisation connected with
the American Chemical
Society which abstracts the world's chemical literature.
CCD
Cambridge Crystallographic Database (also called CCDC for
Cambridge Crystallographic Data Centre)
CFF93
A molecular mechanics force field
CHARMm
A molecular mechanics force field
Chemical
Informatics
'Computer-assisted storage, retrieval and analysis of
chemical information, from data to chemical knowledge.' Chem.
Inf. Lett. 2003, 6, 14. This definition
is distinct from 'Chemoinformatics'
(and the synonymous cheminformatics and chemiinformatics) which focus
on drug design.
Chemiinformatics
See Chemoinformatics
and Chemical
Informatics
Cheminformatics
See Chemoinformatics
and Chemical
Informatics
Chemoinformatics
'The mixing of those information resources [information
technology and information management] to transform data into
information and information into knowledge for the intended purpose of
making better decisions faster in the arena of drug lead identification
and optimization.' (Frank K Brown 'Chemoinformatics: what is it and how
does it impact drug discovery.' Ann. Rep. Med. Chem.
1998, 33, 375-384.) This article also says that chemometrics
is a subset of chemoinformatics. See also Chemical
Informatics, which includes chemoinformatics and also
encompasses areas of chemistry outside drug design.
Chemometrics
Statistical analysis of chemical data
CIF
Crystallographic Information File. A standard format to
exchange crystallographic information
CML
Chemical Markup Language; a SGML for chemistry, designed by
Peter Murray-Rust. A browser is available, called JUMBO
CNDO
Complete Neglect of Differential Overlap. A semi-empirical
molecular orbital method
CODATA
Committee on Data for Science and Technology
COMFA
Comparative Molecular Field Analysis: a 3D-QSAR technique,
which explores molecular fields around a molecule. (Cramer, R. D.;
Patterson, D. E.; Bunce, J. D. J. Am. Chem. Soc.
1988, 110, 5959-5967.
Concord
A program, developed by Robert
Pearlman for generating 3D structures from 2D, distributed by
Tripos.
CORBA
Common Object Request Broker Architecture
CORINA
A program from the Gasteiger Group at Erlangen, which
automatically generates 3D molecular structures from 2D information
COSMIC
A molecular mechanics force field, and also a molecular
modelling program
CPK
Corey, Pauling and Kulton design for plastic models of
molecules
CVFF
Consistent Valence Force Field. See CFF93
DFT
Density Functional Theory. A new approach to molecular
orbital theory
DNA
Deoxyribonucleic acid
DOM
Document Object Model
DOS
Disk Operating System. MicroSoft's operating system for PCs
which has grown into Windows.
DOS
Denial of Service: Computers can be attacked to prevent them
providing access to their resources. More
information is available from CERT.
DREIDING
A molecular mechanics force field
dtd
Document Type Definition. This is an explanation of all the
label that may be used in a SGML.
Dublin
Core
The Dublin Core is a set of core elements which can usefully
be used to structure metadata. The name comes from a workshop in Dublin, Ohio.
Eadfrith
Eadfrith is a free program which produces high-quality
pictures of molecules.
ECEPP
A molecular mechanics force field
ExPASy
ExPASy (Expert Protein Analysis System) proteomics server of
the Swiss Institute of Bioinformatics (SIB)
FEP
Free Energy Perturbation
GAMESS
An ab initio molecular orbital theory package
Gaussian
An ab initio molecular orbital theory package
Global minimum
The lowest energy point on a potential energy surface
Globus
The Globus project provides a toolkit, software tools that
make it easier to build computational grids and grid-based
applications.
GPL
GNU
General Public License. How can a program be licensed as free software?
GPL is one answer.
GRID
A program for finding binding sites on biologically important
macromolecules, developed by Peter Goodford (J. Med. Chem.
1985, 28, 849-857).
GRID
Computational
Grids enable computation as well as data to be shared over a
network of computers.
GROMACS
A molecular dynamics package, primarily designed for
biochemical molecules like proteins and lipids
GROMOS
A molecular mechanics force field
Hessian
A matrix of the second derivatives of energy with respect to
molecular coordinates. The Hessian can be used to determine whether a
stationary point is a minimum, a transition state with one negative
normal mode or a higher order saddle point.
HOMO
Highest Occupied Molecular Orbital
HTML
Hyper Text Mark up Language. This is the language that WWW
browsers understand
http
Hypertext Transfer Protocol
ICSTI
International Council for Scientific and Technical
Information
IUBMB
International Union of Biochemistry and Molecular Biology
IUPAC
International Union of Pure and Applied Chemistry
Java
A computer language which was designed with World-Wide
web-applications particularly in mind
Javascript
A A client-side HTML embedded scripting language for
World-Wide Web browsers, which is not closely related to Java.
Journal
Abbreviations
Chemistry journals have standard abbreviations, which are
listed at the University of British Columbia website
JCAMP
The Joint Committee on Atomic and Molecular Physical Data
developed standard data formats. The work has now been taken over by
IUPAC. JCAMP formats are used for NMR, Mass Spectrometry and other
spectral data.
KEGG
Kyoto Encyclopedia of Genes and Genomes
LCAO
Linear combinations of atomic orbitals. A technique used to
build up molecular orbitals.
LDA
Lithium diisopropylamide: a strong, non-nucleophilic base
LDAP
Lightweight Directory Access Protocol. See, for example, the OpenLDAP
project
Lhasa
Lhasa is a program to help plan organic syntheses, originally
developed by E J Corey at Harvard.
Local minimum
A structure that is minimised with respect to all its
coordinates, but higher in energy than the global minimum
LUMO
Lowest Unoccupied Molecular Orbital
MacroModel
A molecular modelling program (Mohamadi, F.; Richards, N. G.
J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.;
Hendrickson, T.; Still, W. C. "MacroModel- an Integrated Software
System for Modeling Organic and Bioorganic Molecules using Molecular
Mechanics" J. Comp. Chem. 1990, 11,
440-467.)
Magnus
Magnus is a group of programs for doing chemical calculations
and handling chemical information. Most of the programs will run within
a web browser.
MC
Monte Carlo. The name for any of a wide range of stochastic
methods which involve random numbers, or even a mountain with a casino.
The meaning may be clear from the context.
MD
Molecular Dynamics
MIME
Multipurpose Internet Mail Extension. A MIME-type describes
the sort of information that a mail message, or other computer file,
contains, and so a computer knows whether to expect an image, a
molecule, or a spectrum, for example.
MINDO/3
A semi-empirical molecular orbital method
MM2, MM3, MM4
Molecular mechanics force fields
MM2*
MM2 as implemented in MacroModel
MMFF
A molecular mechanics force field
MNDO
A semi-empirical molecular orbital method
MOL
The MOL file format is
defined by MDL (Molecular Design Ltd). A MOL file can describe a
chemical structure, but no properties and references. For further
detail, see the manual 'MDL CTfile Formats' provided by MDL. MOLFile Structure/Data
File is a file
format from MDL
MOPAC
A semi-empirical molecular orbital program
MP2
Second order Mшller-Plesset correction to a Hartree Fock
calculation
mSQL
A lightweight database engine developed by David Hughes
Multiplicity
A measure of the number of unpaired electrons in a molecule.
Singlet multiplicity means that all the electron spins are paired, a
doublet must have one unpaired spin.
MySQL
An open-source database management system, available under
GPL (Gnu General Public License), developed by Monty Widenius.
NCE
New Chemical Entity
NCI
National Cancer Institute: a part of the NIH (qv)
NIH
National Institutes of Health, USA
NIST
National Institute of Standards and Technology, USA
NSF
National Science Foundation
nOe
Nuclear Overhauser Effect. Used in NMR spectroscopy to
determine which atoms are close to each other
OASIS
Organization for the Advancement of Structured Information
Standards (OASIS), is a non-profit, international consortium that
creates interoperable industry specifications based on public standards
such as XML and SGML (See OMG).
OMG
The Object Management Group (OMG) is an open membership,
not-for-profit organisation that produces and maintains computer
industry specifications. Its specifications include CORBA and UML.
OPLS
A molecular mechanics force field
Oracle
The world's leading supplier of software for information
management, and the world's second largest independent software
company. The Oracle database, which uses SQL, is being made
increasingly internet aware.
P2P
Peer-to-peer: a concept for networking computers, used by Gnutella and
other applications.
P3P
Platform for Privacy Preferences Project (P3P), not to be
confused with P2P, is a simple, automated way for users to gain more
control over the use of personal information, developed by the World
Wide Web Consortium.
PCA
Principal
Component Analysis. A set of variables which may be
correlated are transformed to a smaller set of uncorrelated variables.
PCR
Polymerase Chain Reaction
PCR
Principal
Component Regression. A combination of principal component
analysis (PCA) with a regression analysis.
PDB
Protein Data Bank, formerly the Brookhaven Protein Data Bank
PDF
Portable Document Format.
Perl
Perl is a interpreted language optimized for scanning text
files, extracting information and printing reports.
PHP
PHP: Hypertext Preprocessor. A server-side HTML embedded
scripting language, closely connected to database access. PHP offers
compatibility witha number of SQL database servers. Its syntax is
borrowed from C, Java and Perl.
PLS
Partial Least Squares. A fitting
algorithm closely related to principal component regression
(PCR)
PM3
Parameterised Model 3. A Semi-Empirical Molecular Orbital
Theory Hamiltonian, developed by Stewart
PostgreSQL
PostgreSQL is an open-source object-relational database
management system.
PRCG
Polak-Ribiere Conjugate Gradient algorithm for minimisation
QM
Quantum Mechanics
QSAR
Quantitative Structure Activity Relationship
RDBMS
Relational Database Management System
RDF
Radial Distribution Function
RDF
Resource Description Framework: a foundation for processing
metadata providing interoperability between applications that exchange
machine-understandable information on the Web
RDF
RDFile (reaction-data file) is a file
format from MDL.
RFP
Request for proposals. The OMG
periodically issues requests for proposals for standards in data
exchange and interoperable applications
RHF
Restricted Hartree Fock. Useful approximation in ab initio
molecular orbital theory, forcing all electrons to be paired
SCF
Self Consistent Field. Use in molecular orbital theory
SDF
The SDF file format is
defined by MDL (Molecular Design Ltd). A SDF file can contain multiple
compounds together with properties and references. For further detail,
see the manual 'MDL CTfile Formats' provided by MDL.
SDFile Structure/Data File is a file
format from MDL
SELF
Standard Electronic Data Files: developed at a IUCOSPED
meeting, a IUPAC task
group chaired by Dr
Henry Kehiaian
SGML
Standard Generalised Mark-up language. HTML is an SGML with a
particular dtd.
SHAKE
A method of speeding up molecular dynamics simulations by
constraining C-H bond lengths
Simplex
A simple, minimisation algorithm which does not require the
calculation of derivatives
SNP
Single Nucleotide Polymorphisms. DNA sequence variations
SN1
Substitution, Nucleophilic, Unimolecular
SN2
Substitution, Nucleophilic, Bimolecular
SOMO
Semi-occupied molecular orbital - Used instead of HOMO or
LUMO when the highest occupied orbital contains only one electron.
Spartan
An ab initio molecular orbital theory
package
SQL
Structured query language: a language for interacting with
relational databases including Oracle, MySQL, PostgreSQL, and mSQL.
There are several dialects of SQL, and a standardisation
process. SQL can be used for a variety of tasks including:
querying data, updating and deleting rows in a table, altering objects,
controlling access to a database and ensuring database consistency.
STO
Slater Type Atomic Orbital: An early basis set for molecular
orbital theory. These are close in shape to atomic orbitals, but much
harder to manipulate mathematically than gaussian functions, so the
latter are now used almost exclusively.
SVG
Scalable Vector Graphics, a graphics format from Adobe.
SWISS-PROT
A curated protein sequence database which strives to provide
a high level of annotations (such as the description of the function of
a protein, its domains structure, its domains structure,
post-translational modifications, variants, etc.), a minimal level of
redundancy and high level of integration with other databases
TIP3P, TIP4P
Models for the properties of water molecules (Jorgensen, W.
L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L.
"Comparison of Simple Potential Functions for Simulating Liquid Water"
J.
Chem. Phys. 1983, 79, 926-935.)
Tripos
A molecular mechanics force field
UFF
A molecular mechanics force field
UHF
Unrestricted Hartee-Fock. Unlike RHF, this permits a system
to have any multiplicity. Can lead to spin contamination
URL
Uniform Resource Locator- the address of a WWW page
WWW
World Wide Web
XED
Extended Electron Distribution (Vinter, J. G. Extended
electron distributions applied to the molecular mechanics of some
intermolecular interactions J Comp.-Aided. Mol. Design
1994, 8, 653-668.)
XML
Extensible Markup Language: a unified format for structured
documents and data on the web. A less general, and perhaps more useful,
SGML.
Z-matrix
An internal coordinate description of a molecule
