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SCOP (Structural Classification of Proteins)  Classification of protein structure, based

on structure and sequence and involving direct expert analysis by protein structure experts

(in particular Alexey Murzin). There was initially the classical database (https://scop.mrc-

lmb.cam.ac.uk/legacy/). A comprehensive reclassification is SCOP2 (https://scop.mrc-

lmb.cam.ac.uk). For practical use (protein structure prediction and classification), SCOPe

(Structural Classification of Proteins  – extended; https://scop.berkeley.edu) at the

University of Berkeley (Universität Berkeley) is recommended, because the old classifica­

tion is simply extended and, for example, the ASTRAL structure databases are also used. 

Second Gödel’s Incompleteness Theorem  shows that sufficiently strong noncontradic­

tory systems cannot prove their own noncontradiction (a computer thus remains in the

undecidable). The outstanding mathematician Kurt Gödel (1906–1978) deserves credit for

proving, by means of mathematics, the existence of fixed limits for formal systems. 

Secondary Databases  Databases that integrate data and information from primary data­

bases and use them for further analyses, such as protein sequences for predicting protein

structures or domains. 

Secondary Metabolism  Primary metabolites are central to metabolism and are found in

many or nearly all (central metabolites) organisms. In particular, primary metabolism

includes central carbohydrate metabolism (glycolysis, pentose phosphate pathway, and

citric acid cycle), lipid metabolism (synthesis and beta-oxidation), and amino acid synthe­

sis and degradation, as well as nucleotide production, degradation, and recycling (sal­

vage). Secondary metabolites are additional metabolites that only occur in specific

organisms and then have specific effects (pharmacological, neurotransmitters, ecological,

signalling, etc.). 

Secondary Structure  In proteins, two important secondary structures, helices and beta

strands, form from the sequence (also called primary sequence or primary structure) via

hydrogen bonds. The latter can also assemble into beta-sheets. Here we can distinguish

parallel and antiparallel ones, in the case of helices the frequent alpha helices (every 3.6

amino acids one turn; i to i + 4 hydrogen bond, discovered by Pauling) and narrower ones

(310-helix, every 3 amino acids one turn; i to i + 3 bridge) and wider ones (pi-helix, every

4 amino acids one turn, i to i + 5 bridge). The secondary structure can be subdivided much

more finely. Loops, the third type of secondary structure, are also more finely divided into

bends, disordered regions, and typical loops. RNA also forms secondary structures, espe­

cially loops, stems, and pseudoknots (loop contact; true, stable knots would block RNA

and do not occur in biology).

Sequence Comparison  Two sequences are compared by contrasting which amino acid

residues are altered and which are conserved. You can either compare over the whole

length (see global alignment), which is especially good for phylogenetic analyses, or only

a piece (see local alignment), which is especially good to catch a local piece that is particu­

larly similar, especially the domain that has the highest sequence similarity, i.e. a charac­

18  Glossary