Documentation:Glossary

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Some luddites claim that scientists use jargon to create a pseudoelite group of people who use the jargon to exclude people who are not "properly initiated". There does seem to be a human propensity to engage in such behaviour which is rather unfortunate since our goal should be to make our science and research accessible to as many people as possible. So to demystify our communications, we have created this list of terms commonly used by our group to discuss our research. You can see by this expanding list that the luddites may have a point, but at the same time such a list refutes their position.

All terms listed in alphabetical order with acronyms listed first followed by abbreviations. Term descriptions are self contained, meaning that all the information to understand what the term means is given in the description. References to redundant and similar terms are given when relevant. Each description, beyond the expansion of an acronym or abbreviation is ideally no more than one sentence. Needless to say, the group philosophies and style guidelines should be strictly followed. The glossary should be of the very best quality, better than what one would see in journal publications (which we will achieve iteratively; this is simply stated as a reference to the expected quality). The descriptions should be crisp, concise, clear, and simple. Each term is categorised as an abbreviation (ab), acronym (ac), and/or original (or) where relevant. Some overlap between conventions for the terms and the style guidelines is acceptable. Well known terms (for example, "USA") are generally not listed here.

This document is in progress. ... (ellipses) indicates description is to be filled in. Add links to Wikipedia entries that are more explanatory (can be done automagically with a CGI script)?"

Contents

Terms

1

  • 1KP. 1000 Plant transcriptomes/proteomes. ... (ac/ab)

A

  • AA. Amino Acid, repeating molecular units that make up proteins. There are 20 of them that commonly occur in nature. (ac)
  • ab initio. Latin for "from the beginning". Used to refer to methods which do not use large contiguous templates for structure prediction.

B

  • BLAST. Basic Local Alignment Search Tool. An algorithm which finds protein and nucleic acid sequence alignments. (ac)
  • BBA. Biophysics Based Approach. An approach that is based on biophysics primarily. See also KBA. (ac)
  • BP. Base Pair. Intermolecular hydrogen bonding interactions between purine (larger double ringed, i.e., Adenine and Guanine) and pyrimidine (smaller single ringed, i.e, Cytosine and Thymine/Uracil) nitrogenous base pairs in NA (DNA/RNA) interactions. Pairs composed of Adenine:Thymine (A:T), or Adenine:Uracil (A:U) in RNA, have two hydrogen bonds and pairs composed of Guanine:Cytosine (G:C) base pair have three hydrogen bonds between them. The nucleotide pairing is usually strict with the hydrogen bonds regulating the stability of double stranded interactions and whether strand pairing is a constant or if they need to be taken apart and put back together. Exemptions are uncommon and are also related to an evolutionary adaptation. For example, G:U pairings are seen in RNA due to the "wobble" effect and play a key role in regulating the use of transfer RNAs during translation. (ac)
  • BTM. Beta Thalassemia Major. The worst form of Beta Thalassemia. (ac)

C

  • CANDO. Computational Analysis of Novel Drug Opportunities. ... (ac+or)
  • CASP. Critical Assessment of protein Structure Prediction methods. [One sentence description; note historical use of it being both an acronym and abbreviation.] (ab+ac)
  • CSD. Cambridge Structural Database. Repository of high resolution small molecule and peptide structures. (ac)
  • CWR. Consensus Weighted Rank. See our Trends in Pharmacological Sciences paper from 2008. (ac)
  • clinical trial. ... See also phase {0-5} clinical trial, preclinical studies.

D

  • DEA. Drug Enforcement Agency. ... (ac)

F

  • FAD. FDA Approved Drugs. Drugs that are completely FDA approved. (ac)
  • FDA. Food and Drug Administration. ... (ac)

H

  • HIC. Human Ingestible Compound. Typically a small molecule compound that is known to be relatively safe to ingest by humans (relative according to ...). (ac)

I

  • IF. Impact Factor. ... (ac)
  • IFU. Independent Folding Unit. ... (ac)
  • IND. Investigational New Drug. ... (ac)

J

  • JIT. Just In Time. Information requested by the NIH on other current and pending support typically to determine if and how to make an award. (ac)

K

  • KBA, IBA. Knowledge Based Approach or Informatics Based Approach. See also BBA. (ac)
  • KBP, KBF. Knowledge Based Potential or Knowledge Based Forcefield. See also RAP. (ac)

M

  • MFS. Meta Functional Signature. Method to assess functional importance of particular residues in a protein (ac)
  • MOU. Memoram Of Understanding. A document that lays out the "contract" between two institutions when PIs from them collaborate. (ac)
  • MPU. Minimum publishable unit. The minimum multidimensional requirement (in terms of concept, results, impact, etc.) needed to publish a manuscript. (ac)
  • MS3D. Mass Spectroscopy in 3 Dimensions. ... See also SSP. (ab+ac)
  • MSA. Multiple Sequence Alignment. An simultaneous alignment between several protein or nucleic acid chains (ac)
  • mcgen. Main chain generation. The prefix for a group of programs in the RAMP suite which model main chains of proteins. (ab)
  • M tb. Mycobacterium tuberculosis. A convenient abbreviation for the pathogen. (ab)

N

  • NA. Nucleic Acid, repeating molecular units that make up DNA and RNA. (ac)
  • NCE. Novel Chemical Entity. ... (ac)
  • NIH. National Institutes of Health. ... (ac)
  • NR. NonRedundant. Any non redundant set of objects. (ac)
  • NRW. Nutritious Rice for the World. ... See also 1KP. (ac)
  • NSF. National Science Foundation. ... (ac)

O

  • OSP. Office of Sponsored Programs. The unit responsible for handling grants, contracts, and other extramural awards made to support a given PI's research. It was formerly known as the Grants and Contracts Agency (GCA) at the UW. (ac)

P

  • PA. Program Announcement. Solicitation from a funding agency for grant applications in a particular field of research or under a particular funding program. See also RFA, RFP. (ac)
  • PDB. Protein Data Bank, worldwide repository for solved experimental protein structures. (ac)
  • peptide. A short amino acid chain. Usually used to refer to chains <20 amino acids.
  • PiHKAL. Phenethylamines i Have Known and Loved. ... See also phenethylamine, TiHKAL, tryptamine. (ac)
  • PI. Principal Investigator. The principal (meaning primary) investigator usually refers to the head of a laboratory or a group with the ability to write and submit grants and contracts in conjunction with the OSP. Some people prefer to expand the P in PI to mean "principle" as in a scientific goal or aim; this is not the official NIH expansion of the term. (ac)
  • PITA. Pain In The A***. Needs no description; to paraphrase US Supreme Court Justice Potter Stewart, you'll know it when you see it. Synonym with "troublemaker". See also SD. (ac)
  • PFF, PPF. Polarisable Force Field or Polarisable Potential Function. A potential function that attempts to handle polarisability. (ac)
  • PCC. Protein compound complex. ... (ac)
    • PCI Protein compound interaction. ... (ac)
    • PCIN Protein compound interaction network. ... (ac)
  • PNA. Protein Nucleic Acid {Complex,Interaction,Network}. A complex (typically 3D atomic level) or interaction or network between a protein and a nucleic acid (NA) molecule, typically protein-DNA or protein-RNA {Complex,Interaction,Network}.
    • PNAC. Protein Nucleic Acid Complex. A "complex" usually refers to a 3D atomic level protein-DNA protein-RNA interaction. (ac)
    • PNAI. Protein Nucleic Acid Interaction. An "interaction" in this context may or may not be determined at the 3D atomic level. (ac)
    • PNAN. Protein Nucleic Acid Network. A network composed of protein-DNA and protein-RNA interactions. (ac)
  • PPC. Protein protein complex. ... (ac)
    • PPI. Protein protein interaction. ... (ac)
    • PPIN. Protein protein interaction network. .... (ac)
  • PU. Publishable unit. ... see also MPU. (ac)
  • phase {0-5} clinical trial. ...
  • phenethylamines. ..
  • preclinical studies. ...
  • psychedelic, psychoactive, psychopharmaceutical, psychotropic. A chemical substance that crosses the blood–brain barrier and acts primarily upon the central nervous system where it affects brain function, resulting in changes in perception, mood, consciousness, cognition, and behavior.

R

  • RAMP. Rapid Auto Modelling of Proteins (or anything else, like RAM's Programs). A suite of programs to aid modeling protein structure. (ac)
  • RAP, GRAP, IRAP. General abstract terms representing all atom discriminatory functions. See also RAPDF. (ab+ac)
    • RAP. RAP is A Potential (recursive) or Residue specific All atom Potential; currently RAPDF. (ac)
    • GRAP. Generalised RAP; currently BTTR. (ac)
    • IRAP. Interaction RAP; currently BTTR. (ac)
  • RAPDF, IRAPDF, RVPDF, NVPDF, AEFI, BTTR. A variety of Bayesian conditional probability discriminatory functions. See also RAP, IRAP. (ab+ac)
    • RAPDF. Residue specific All atom Probability Discriminatory Function. By default it is a pairwise atomic distance function covering 18 bins ranging from 0-20 A in 1 A increments except for the first 0-3 A bin, plus 167 atom types. (ac)
    • IRAPDF. Interaction Residue specific All atom Probability Discriminatory Function. ... (ac)
    • RVPDF. Residue specific Virtual atom Probability Discriminatory Function. ... (ac)
    • NVPDF. Nonresidue specific Virtual atom Probability Discriminatory Function. ... (ac)
    • AEFI. ... Similar to BTTR but contains a geometric orientation term. (ac)
    • BTTR. Better Than The Rest. A generalized knowledge-based discriminatory function for biomolecular interactions. (ac)
      • RMR6. ... The best parameterised version of BTTR. (ac)
  • Residue. See Amino Acid.
  • RFA. Request For Applications. Solicitation from a funding agency for grant applications in a particular field of research or under a particular funding program. See also PA, RFP. (ac)
  • RFP. Request For Proposals. Solicitation from a funding agency for grant applications in a particular field of research or under a particular funding program. See also PA, RFA. (ac)
  • RMSD. Root Mean Squared Deviation. A measure of the average distance between atoms of superimposed protein structures. (ac)
  • ROA. Route Of Administration. A general term usually applicable to how a compound/therapeutic is administered. (ac)
  • RMSD. Root Mean Squared Deviation. An measure of the average distance between atoms of (superimposed) protein structures. (ac)
    • ARMSD, AaRMSD. All atom RMSD. Considers all (side chain and main chain) atom positions for calculating the RMSD. (ab+ac)
    • CRMSD, CaRMSD. C alpha RMSD. Considers only Ca atom positions. (ab+ac)
    • MRMSD, McRMSD. Main chain RMSD. Considers only main chain atom positions and consequently does not take into consideration deviation in side chain positions. (ab+ac)
    • SRMSD, ScRMSD. Side chain RMSD. Considers only side chain atom positions and consequently does not take into consideration deviation in main chain positions. (ab+ac)
  • RTFM. Read The Flippin' Manual. An instruction given when it is believed that a query may readily answered by reading pertinent documentation (or instruction manual). See also UTSE. (ac)

S

  • SD. S*** Disturb(er). Needs no description; to paraphrase US Supreme Court Justice Potter Stewart, you'll know it when you see it. Synonym with "troublemaker". (ac)
  • SS. Secondary Structure. Refers to the characteristic structures that amino acid chains form into due to favorable local interactions in the main chain. The most common secondary structures are alpha helices and beta sheets. (ac)
  • SSP. Shotgun Structural Proteomics. ... See also MS3D. (ac)
  • scgen. Side chain generation. The prefix for a group of programs in the RAMP suite which model the side chains of proteins. (ab)
  • schedule {1-5}. ...

T

  • TB. Tuberculosis. Just a convenient abbreviation for tuberculosis (the disease, not the organism, though see M tb. (ab)
  • TiHKAL. Tryptamines i Have Known and Loved. ... See also phenethylamine, PiHKAL, tryptamine. (ac)
  • TT. Transtarget. A protein, or other, molecule, implicated in the action of a particular compound on an organism which could be a target (implicated by direct desirable binding of compound), antitarget (implicated by direct undesirable binding), or offtarget (implicated by direct or indirect binding to nontargets). (ac)
  • tryptamine. One of the 20 naturally occurring amino acids. Characterized by its nitrogen containing aromatic ring system and general bulkiness.

U

  • UTSE, UTFSE. Use The (Flippin') Search Engine. An instruction given when a query may be readily answered by using a search engine. The "F" is optional. See also RTFM. (ac)
  • UW. University of Washington.

Conventions

  • Gene names are mostly lowercase and are italicised (for example: lacZ). Protein names are in uppercase and sometimes bolded (for example: LACZ).
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