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Protocols

Kojak specifications

Information


Unique identifier OMICS_08032
Name Kojak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License Apache License version 2.0
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Robert L. Moritz

Publication for Kojak

Kojak citations

 (7)
library_books

Participation to the first Cybathlon: an overview of the FREEWHEELS team FES cycling solution

2017
PMCID: 5745382
PMID: 29299223
DOI: 10.4081/ejtm.2017.7120

[…] ICE trike was initially equipped with a 26” rear wheel, we changed for a 24” one to tilt the bike and elevate the crank relatively to the pilot’s position (). Low rolling resistance tires (Schwalbe® Kojak 24 x 1.35”) were also mounted instead of the original tires.A few weeks before Cybathlon competition we decided to modify the rear wheel transmission, initially a freewheel, to a fixed-gear. Thi […]

library_books

Solving protein structures using short distance cross linking constraints as a guide for discrete molecular dynamics simulations

2017
Sci Adv
PMCID: 5501500
PMID: 28695211
DOI: 10.1126/sciadv.1700479

[…] ode. For MS/MS, the collision energy was set to 35%. Data were analyzed using the DXMSMS Match program from our ICC-CLASS (Isotopically Coded Cleavable Cross-Linking Analysis Software Suite), or with Kojak (). For scoring and assignment of the MS/MS spectra, b and y ions were primarily used, with additional confirmation from collision-induced dissociation cleavage of the cross-linker, whenever thi […]

call_split

The Ndc80 complex bridges two Dam1 complex rings

2017
eLife
PMCID: 5354518
PMID: 28191870
DOI: 10.7554/eLife.21069.038
call_split See protocol

[…] into mzML using msconvert from ProteoWizard (). Standard linear peptide searches were performed using Comet to identify all proteins in the sample (). Cross-linked peptides were identified using the Kojak version 1.4.2 cross-link identification software () following the author’s instructions (http://www.kojak-ms.org). Kojak results were exported to Percolator version 2.08 () to produce a statisti […]

library_books

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

2016
eLife
PMCID: 5127641
PMID: 27805565
DOI: 10.7554/eLife.20352.031

[…] re with shaking. Digested samples were acidified with 5M HCl prior to being stored at −80°C until analysis. MS analysis was performed on a Q-Exactive (Thermo Fisher Scientific) and analyzed using the Kojak (version 1.4.2) cross-link identification software as previously described (; ). […]

library_books

The molecular architecture of the Dam1 kinetochore complex is defined by cross linking based structural modelling

2015
Nat Commun
PMCID: 4660060
PMID: 26560693
DOI: 10.1038/ncomms9673

[…] he search databases for γTuSC, BARD1/BRCA1, SCFFBXL3, free Dam1 complex and Dam1 complex on MTs. MSDaPl was used to visually inspect the Comet results. Cross-linked peptides were identified using the Kojak version 1.0 cross-link identification software following the author's instructions (http://www.kojak-ms.org) and using the search parameters outlined in . Kojak results were exported to Percolat […]

library_books

Comparative Assessment of Blood Lead Levels of Automobile Technicians in Organised and Roadside Garages in Lagos, Nigeria

2015
PMCID: 4338385
PMID: 25759723
DOI: 10.1155/2015/976563

[…] ted over the weekends. All medical wastes such as used swabs and gloves were collected into appropriately labelled disposable bags. Sharp objects were put into disposable biological waste containers (Kojak Safety box) and sealed as per manufacturer's instructions.All the blood samples collected from subjects from both groups were analysed at the Department of Chemistry of the University of Lagos l […]

Citations

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Kojak institution(s)
Institute for Systems Biology, Seattle, WA, USA
Kojak funding source(s)
This work was partially supported with federal funds from the National Science Foundation MRI grant no. 0923536 and from the National Institutes of Health National Institute of General Medical Sciences under grant nos. 2P50 GM076547/Center for Systems Biology, GM087221, S10RR027584, and P41 GM103533.

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