Xwalk statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Xwalk
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Tool usage distribution map

This map represents all the scientific publications referring to Xwalk per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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


A registration is needed to download tool.

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

Versioning


No version available

Maintainers


  • person_outline Ruedi Aebersold
  • person_outline Abdullah Kahraman

Additional information


A registration is needed to download tool.

Publication for Xwalk

Xwalk citations

 (11)
library_books

Protein Tertiary Structure by Crosslinking/Mass Spectrometry

2018
Trends Biochem Sci
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) , . These solvent-accessi […]

library_books

Capturing protein communities by structural proteomics in a thermophilic eukaryote

2017
Mol Syst Biol
PMCID: 5527848
PMID: 28743795
DOI: 10.15252/msb.20167412

[…] ferred 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. […]

call_split

Cross linking mass spectrometry identifies new interfaces of Augmin required to localise the γ tubulin ring complex to the mitotic spindle

2017
PMCID: 5450317
PMID: 28351835
DOI: 10.1242/bio.022905
call_split See protocol

[…] al. 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 the shortes […]

library_books

Blind testing of cross‐linking/mass spectrometry hybrid methods in CASP11

2016
Proteins
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 distanc […]

call_split

Critical Assessment of Protein Cross Linking and Molecular Docking: An Updated Model for the Interaction Between Photosystem II and Psb27

2016
Front Plant Sci
PMCID: 4758025
PMID: 26925076
DOI: 10.3389/fpls.2016.00157
call_split See protocol

[…] The high-resolution crystal structure of mature PSII should facilitate an in silico approach to the prediction of potential cross-links in the protein complex. We used the Xwalk algorithm () to calculate solvent-accessible surface distances between lysine residues in PSII. Potential cross-links were limited to a maximum distance of 35 Å, as the distance constraint for B […]

call_split

X ray, Cryo EM, and computationally predicted protein structures used in integrative modeling of HIV Env glycoprotein gp120 in complex with CD4 and 17b

2016
PMCID: 4749890
PMID: 26937457
DOI: 10.1016/j.dib.2016.01.001
call_split See protocol

[…] nformation is available in the folder bindingfootprints.Chemical cross-linking is often used to generate low resolution distance constraints between parts of a protein (or multiple proteins). We used Xwalk , a computational tool that mimics cross-linking experiments by calculating the distance between two residues along the surface of the proteins, to identify inter-domain(gp120-CD4 and gp120-17b) […]


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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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