Computational protocol: Viral Capsid Proteins Are Segregated in Structural Fold Space

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Protocol publication

[…] We chose the Template Modeling-score (TM-score) as our structural comparison metric, for the following reasons. This structure-alignment-based scoring function using the fr-TM-align algorithm is very fast to compute and suits our large-scale comparison; it is normalized, or protein size independent, making the comparison between pairs of domains with complex topology and pairs with simpler ones fair; it has been established in large scale benchmark studies that most of the pairs of proteins with a TM-score of more than 0.5 have the same fold classification, and most of those with a TM-score of less than 0.5 are in different fold classes . In addition, a TM-score of 0.4 has also been extensively used as a criterion to decide if a pair of structures are similar or not . Given that many proteins within the same SCOP fold can have a TM-score of 0.4 and higher, we chose the TM-score of 0.4 as the threshold to validate our hypothesis.Briefly, the structural alignment score is defined aswhere LN and LT are the lengths of the two peptides being compared, di is the distance between the Cα atoms of the structurally equivalent residues, and d0 is a normalization score to make the alignment length-independent. The term Max stands for an optimal superimposition between the two structures to minimize distances between structurally-equivalent residues. We define structural distance between a pair of proteins by (1–TM-score), which ranges from zero to one. […]

Pipeline specifications

Software tools TM-Score, Fr-TM-align
Application Protein structure analysis