ARP/wARP protocols

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ARP/wARP specifications

Information


Unique identifier OMICS_15564
Name ARP/wARP
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format MTZ
Computer skills Basic
Version 7.6
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anastassis Perrakis <>

Information


Unique identifier OMICS_15564
Name ARP/wARP
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Medium
Version 7.6
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Anastassis Perrakis <>

Publications for ARP/wARP

ARP/wARP in pipelines

 (54)
2018
PMCID: 5766984
PMID: 29344086
DOI: 10.1186/s13068-017-1006-7

[…] by r and rfree calculations, 5% of the data were excluded from the structure refinement []. solvent molecules were automatically added using the automatic water picking function in the arp/warp package []. picked water molecules were selected or discarded manually by visual inspection of 2fo–fc and fo–fc electron density maps. the coordinates for the two final tatcel7a_cd structure […]

2018
PMCID: 5851995
PMID: 29540745
DOI: 10.1038/s41598-018-22842-4

[…] of a truncated lc/b (pdb code 1epw) as a search model in phaser. the working models were refined using refmac5 and manually adjusted with coot. water molecules were added with the help of arp/warp at positions where fo−fc electron density peaks exceeded 3σ, and potential hydrogen bonds could be made. validation was performed with molprobity. crystallographic data statistics […]

2018
PMCID: 5876331
PMID: 29599493
DOI: 10.1038/s41467-018-03498-0

[…] map for further manual model building. refmac5 was used for structural refinement. intermittent manual building implemented in coot was used to correct and improve the initial models produced by arp/warp. the b-factors were refined with tls corrections (4 tls group, 84 parameters). the final model of pml ring tetramer contains 187 residues and 224 water molecules. ramachandran statistics […]

2017
PMCID: 5289526
PMID: 28152088
DOI: 10.1371/journal.pone.0171056

[…] and stepwise addition of missing residues interspersed with refinement cycles in refmac5 [], until the electron density for the rest of the molecule appeared. the model was completed using arp/warp [] as included in ccp4 []. the manual rebuilding and refinement was continued using coot and refmac5. a randomly chosen set of 5% of the reflections was not used in the refinement, […]

2017
PMCID: 5291390
PMID: 28158290
DOI: 10.1371/journal.pone.0171606

[…] the cbm32-2:galnac complex was determined by single wavelength anomalous dispersion, whereby automated experimental phasing was performed using shelx [] and automated model building was done using arp/warp []. final models of all five structures were obtained using successive rounds of manual model building in coot [] and automated refinement using phenix [] or refmac []. model validation […]


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ARP/wARP in publications

 (657)
PMCID: 5940772
PMID: 29739942
DOI: 10.1038/s41467-018-04214-8

[…] with anomalous scattering. six mercury sites were found and refined with sharp. the resultant map was improved by threefold non-crystallographic averaging and an initial model was built by arp/warp. subsequent refinement was done with refmac. data collection and refinement statistics are listed in supplementary table ., data of human trim25 cc-pryspry crystals were collected on esrf […]

PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] were merged and scaled using blend. semet sites were identified and refined with the programs shelx and sharp,. the phases were further improved by resolve and an initial model was built using the arp/warp web service. the structure from the best-diffracting semet-sad data was determined by phaser to 1.95 å resolution in space group c2. the native data set was processed in xia2 through ccp4i […]

PMCID: 5876331
PMID: 29599493
DOI: 10.1038/s41467-018-03498-0

[…] pml ring. eight zn2+ positions were determined by crunch2 using data between 20 and 1.6 å. an interpretable map was obtained by solvent flattening using program solomon. the autotracing program arp/warp was then used to produce a σa-weighted 2fo-fc map for further manual model building. refmac5 was used for structural refinement. intermittent manual building implemented in coot was used […]

PMCID: 5871880
PMID: 29593291
DOI: 10.1038/s41598-018-23608-8

[…] structures of mettl16_291 were solved by molecular replacement using phaser and the x-ray crystal structure of human methyltransferase 10 domain containing protein (94% identity, pdb id: 2h00). arp/warp was used to build the initial model, which afterwards was placed inside the unit cell with the achesym server. manual fitting in the electron density maps was completed in coot […]

PMCID: 5858766
PMID: 29554129
DOI: 10.1371/journal.pone.0194499

[…] dropped to a value of around 0.21 at full resolution for the structures, based upon both the 2fo–fc and fo–fc electron density maps. solvent molecules were automatically added and refined with arp/warp [] and refmac 5.3., the crystal structure model was used for molecular docking. autodock vina [] was utilized to produce active site-substrate molecular docking solutions for the sat crystal […]


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ARP/wARP institution(s)
Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, Netherlands; Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
ARP/wARP funding source(s)
Supported by the National Institutes of Health (Grant R01 GM62612), the NWO/CW (VENI 700.55.405), the Wellcome Trust (Grant 064405/Z/01/A) and the European Union BIOXHIT FW6 Integrated Project (Grant LSHG-CT-2003-503420).

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