PROFcon: novel prediction of long-range contacts
Bioinformatics
A knot or not a knot? SETting the record 'straight' on proteins
Computational Biology and Chemistry
Ab initio modelling of the N-terminal domain of the secretin receptors
Computational Biology and Chemistry
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The current knowledge on topological knots in protein structure is reviewed, considering in turn, knots with three, four and five strand crossings. The latter is the most recent to be identified and has two distinct topological forms. The knot observed in the protein structure is the form that requires the least number of strand crossings to become un-knotted. The position of the chain termini must also correspond to a position that allows (un) knotting in one move. This is postulated as a general property of protein knots and other more complex knots with this property are proposed as the next most likely knots that might be found in a protein. It is also noted that the ''Jelly-roll'' fold found in some all-@b proteins would provide likely candidates. Alternative measures of knottedness and entanglement are reviewed, including the occurrence of slip-knots. These measures are related to the complexity of the protein fold and may provide useful filters for selecting predicted model structures.