Crosslinking validation - m3g/xlff GitHub Wiki

Cross-linking data has been usually validated evaluating the Euclidean distance between residues which depends only on the cross-linker length which will define an upper limit indiscriminately of the residues nature. We introduce a statistical analysis which considers the physical nature (the topological distance) of the cross-linking experiment by using Topolink. This distance depends on the cross-linker length and the nature of the residues, as expected. The statistical limits guarantee there will be a confirmation of the two side chain in which the reactive atoms are at the maximum distance defined by the cross-linker.

Reference based on CATH-S40 (V4.1) analysis with Topolink (v17.091) https://gibhub.com/mcubeg/topolink

Linker_name	      Link_Type L[XL] [max] 
DSS/BS3		      KK        11.5  17.8  
DSS/BS3		      KS	11.5  15.8  
DSS/BS3		      SS	11.5  13.4  
1,6-diaminehexane     EE        11.5  15.1  
1,6-diaminehexane     DE	11.5  14.3  
1,6-diaminehexane     DD	11.5  13.5  


DSG                   KK        7.7   15.2  
DSG                   KS        7.7   12.4  
DSG                   SS        7.7   10.0  
1,3-diaminepropane    EE        7.7   11.6  
1,3-diaminepropane    DE        7.7   10.7  
1,3-diaminepropane    DD        7.7   9.8   

zero-length           KD        0.0   9.7   
zero-length           KE        0.0   10.5  
zero-length           SD        0.0   7.0   
zero-length           SE        0.0   7.7