Month: January 2013

I’m pleased to announce the release of OPSIN 1.4.0. This new release brings significant improvements to OPSIN’s coverage of carbohydrate nomenclature. It also complements NextMove Software’s Sugar & Splice project that aims to make the conversion between carbohydrate and small molecule representations effortless.

Below is the effect this improvement to OPSIN has had on the conversion of IUPAC names in ChEBI. (This is one of the data sets used in the OPSIN publication [free access])

Examples of new nomenclature supported (pictures generated by the OPSIN web service)

OPSIN 1.4.0 is available from Bitbucket and Maven Central. The full release notes are below:

• Added support for dialdoses,diketoses,ketoaldoses,alditols,aldonic acids,uronic acids,aldaric acids,glycosides,oligosacchardides, named systematically or from trivial stems, in cyclic or acyclic form
• Added support for ketoses named using dehydro
• Added support for anhydro
• Added more trivial carbohydrate names
• Added support for sn-glcyerol
• Improved heuristics for phospho substitution
• Added hydrazido and anilate suffixes
• Allowed more functional class nomenclature to apply to amino acids
• Added support for inverting CAS names with substituted functional terms e.g. Acetaldehyde, O-methyloxime
• Double substitution of a deoxy chiral centre now uses the CIP rules to decide which substituent replaced the hydroxy group
• Unicode right arrows, superscripts and the soft hyphen are now recognised

The vast majority of amino acid residues that appear in peptides and proteins appear as their natural L-form enantiomer. This is the form of all amino acids as translated by the ribosome. However post-translational modification, such as by racemases, or peptide synthetic methods can be used to introduce the mirror image D-forms of amino acids into peptidic compounds.

Though rare, it is often important to keep track of whether individual amino acids are L-form, D-form, unknown or a racemic mixture of the two (DL-form). Rather unhelpfully, IUPAC rule 3AA-3.3 from IUPAC’s “Nomenclature and Symbolism for amino acids and peptides” states that the configuration prefix may be omitted for amino acids from a natural protein source (where the configuration may be assumed to be L) and for amino acids from synthetic sources (where the configuration is assumed to be an equimolecular mixture of enantiomers).

In the RCSB’s PDB file format, three letter residue codes have been assigned for both the L- form and the D- form of the traditional 19 amino acids other than glycine. Glycine (PDB residue code GLY) has an achiral α-carbon and therefore does not have an L-form and a D-form. For convenience, the table below lists the correspondence between PDB’s three letter codes for these amino acids.

Name	L-form	D-form
Alanine	ALA	DAL
Arginine	ARG	DAR
Asparagine	ASN	DSG
Aspartic Acid	ASP	DAS
Cysteine	CYS	DCY
Glutamine	GLN	DGN
Glutamic Acid	GLU	DGL
Histidine	HIS	DHI
Isoleucine	ILE	DIL
Leucine	LEU	DLE
Lysine	LYS	DLY
Methionine	MET	MED
Phenylalanine	PHE	DPN
Proline	PRO	DPR
Serine	SER	DSN
Threonine	THR	DTH
Tryptophan	TRP	DTR
Tyrosine	TYR	DTY
Valine	VAL	DVA

The above table is believed to be the only internet resource conveniently linking the two PDB residue codes for enantiomeric forms of amino acids.

Unfortunately for the two recent natural amino acids, selenocysteine (PDB residue code CSE) and pyrrolysine (PDB residue code PYH), no PDB residue codes have yet been assigned for their enantiomeric D-forms.

Image credit: The Joneses (where are the joneses on Flickr)