xwalk

Chemical cross-linking of proteins or protein complexes and the mass spectrometry based localization of the cross-linked amino acids is a powerful method for generating distance restraints on the substrate’s topology. Here we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a “Solvent Accessible Surface Distance”, which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.

bin
AvgInterface.class
com
convertUniprot2PDBpos.pl
external
Hes.class
Interface.class
mm
package-info.class
Slider.class
structure
Xwalk.class
xwalk
doc
allclasses-frame.html
allclasses-noframe.html
AvgInterface.html
class-use
com
constant-values.html
deprecated-list.html
external
help-doc.html
index-files
index.html
Interface.html
mm
overview-frame.html
overview-summary.html
overview-tree.html
package-frame.html
package-list
package-summary.html
package-tree.html
package-use.html
resources
serialized-form.html
structure
stylesheet.css
Xwalk.html
xwalk
README
src
com
external
mm
package-info.java
structure
Xwalk.java
xwalk
utils
AvgInterface.java
convertUniprot2PDBpos.pl
Hes.java
Interface.java
Slider.java