Chemical Informatics Letters

Editor: Jonathan M Goodman

Glossary

To suggest a new word for this list, e-mail jmg11@cam.ac.uk with subject line: "CIL glossary: [new word]"

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)
BDNR: 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
MOPAC: A semi-empirical molecular orbital program
MP2: Second order Moller-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
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
S_N1: Substitution, Nucleophilic, Unimolecular
S_N2: 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

You may also want to consult: