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Xwalk specifications

Information


Unique identifier OMICS_18720
Name Xwalk
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Beta
Maintained Yes

Maintainers


  • person_outline Ruedi Aebersold <>
  • person_outline Abdullah Kahraman <>

Additional information


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Information


Unique identifier OMICS_18720
Name Xwalk
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format PDB
Programming languages Java
Computer skills Advanced
Version 0.6
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Ruedi Aebersold <>
  • person_outline Abdullah Kahraman <>

Additional information


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Publication for Xwalk

Xwalk in publications

 (11)
PMCID: 5854373
PMID: 29395654
DOI: 10.1016/j.tibs.2017.12.006

[…] to model this effect and compute the distance between crosslinked residues over the solvent-accessible surface of the protein model instead of computing the euclidean distance between cα atoms , , . xwalk and jwalk put the protein model into a grid and used breadth-first search to find the shortest solvent-accessible surface distance between crosslinked residues (ssasds) , . […]

PMCID: 5954043
PMID: 29476363
DOI: 10.1007/s40273-018-0628-3

[…] copd chronic obstructive pulmonary disease, sd standard deviation, sev order most severe mean value for each condition (where 1 is the most severe), % swd percentage of states worse than dead, xwalk crosswalk, adha attention deficit hyperactivity disorder, copd chronic obstructive pulmonary disease, sd standard deviation, sev order most severe mean value for each condition (where 1 […]

PMCID: 5527848
PMID: 28743795
DOI: 10.15252/msb.20167412

[…] using clusterone (nepusz et al, ). the cross‐linking ld score (walzthoeni et al, ) was calibrated on distance restraints imposed by the cross‐linker. cross‐linking distances were calculated by xwalk (kahraman et al, ) using structural models., prediction of the structure of all 1,176 identified proteins was performed with itasser v4.2 (yang et al, ) and modeller 9v2 (sali & blundell, […]

PMCID: 5450317
PMID: 28351835
DOI: 10.1242/bio.022905

[…] position ‘+1’ refers to a slide by 1 heptad-repeat of dgt5 towards its n-terminus, and ‘−1’ towards its c-terminus. to evaluate which model simulates the experimental data better, we used program xwalk () to calculate distances between beta-carbons of cross-linked lysines (euclidean distance). since such distance vectors can penetrate the surface of the protein, xwalk also computes […]

PMCID: 5042049
PMID: 26945814
DOI: 10.1002/prot.25028

[…] some degree. cross‐links from soluble linkers are formed along the protein surface and therefore scoring functions should take the surface of the protein into account when modeling clms constraints. xwalk uses breath first search on a surface grid to determine the shortest path between two surface points. this approach is shown to be more discriminative than constraints that use euclidian […]


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Xwalk institution(s)
Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
Xwalk funding source(s)
Supported by ETH Zurich; the Commission of the European Communities through the PROSPECTS consortium (EU FP7 projects 201648, 233226); SystemsX.ch – The Swiss Initiative for Systems Biology in part.

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