DIpro protocols

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DIpro specifications

Information


Unique identifier OMICS_04652
Name DIpro
Alternative name DIsulphide bridge prediction
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
SSpro
Maintained Yes

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Documentation


Maintainer


  • person_outline Pierre Baldi <>

Information


Unique identifier OMICS_04652
Name DIpro
Alternative name DIsulphide bridge prediction
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Pierre Baldi <>

Publication for DIsulphide bridge prediction

DIpro in pipeline

2017
PMCID: 5524358
PMID: 28742131
DOI: 10.1371/journal.pone.0181940

[…] and netnglyc (http://www.cbs.dtu.dk/services/netnglyc/), respectively. pfam (http://pfam.janelia.org/) was used to search for protein domains. protein disulfide bonds were predicted using dipro (http://scratch.proteomics.ics.uci.edu/)., molecular modeling of mature ataga and lhaga was done with the phyre server using default parameters (http://www.sbg.bio.ic.ac.uk/phyre2/) []. […]


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DIpro in publications

 (20)
PMCID: 5724701
PMID: 28895153
DOI: 10.1111/nph.14786

[…] or symbiotic. mature zt6 protein (residues 19–137) contains two cysteine residues (residues 36 and 133) which are not predicted to form a disulfide bridge (dianna, scratch protein predictor dipro). this two‐cysteine form of srnase is also found in the majority of most closely related plant‐pathogenic fungal species, including zymoseptoria brevis and pseudocercospora musae, which, like […]

PMCID: 5574707
PMID: 28868356
DOI: 10.1126/sciadv.1603103

[…] then be evaluated from the einstein relation (cm2 v−1 s−1)μh=ekbtd(7)where e is the electronic charge., the transfer integral (v) was calculated using the site-energy correction method () and the dipro approach (). the reorganization energy (λ) was obtained from the sum of the following two energy differences ()λ=λ1+λ2(8)λ1=eeq0*−eeq**(9)λ2=eeq*0−eeq00(10)where eeq0*(eeq**) is the energy […]

PMCID: 5524358
PMID: 28742131
DOI: 10.1371/journal.pone.0181940

[…] and netnglyc (http://www.cbs.dtu.dk/services/netnglyc/), respectively. pfam (http://pfam.janelia.org/) was used to search for protein domains. protein disulfide bonds were predicted using dipro (http://scratch.proteomics.ics.uci.edu/)., molecular modeling of mature ataga and lhaga was done with the phyre server using default parameters (http://www.sbg.bio.ic.ac.uk/phyre2/) []. […]

PMCID: 5390308
PMID: 28234472
DOI: 10.1021/acs.jctc.6b00935

[…] the type of excitation and length-scale on which the transfer occurs, different interactions and mechanisms mediate the coupling, as depicted schematically in ., in this paper, a dimer projection (dipro) method for exciton coupling based on many-body green’s functions theory within the gw approximation and bethe–salpeter equation (gw-bse)− is presented. monomer electron–hole wave functions […]

PMCID: 5333481
PMID: 28255315
DOI: 10.4103/1735-5362.199048

[…] elements’ predictions, jalview and jpred softwares were applied, respectively()., to predict the bonding state of cysteines in hirudin, online software that used the different algorithms, including dipro(), cyspred(), disulfind() and metadetector(), were employed., for this study, the computational methods were employed to determine the best site for cysteine specific pegylation in hv3. hm […]


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DIpro institution(s)
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA
DIpro funding source(s)
This project was supported by the NIH Biomedical Informatics training grant (grant number: LM-07443-01), Grant sponsor: NSF MRI grant; Grant number: EIA-0321390; Grant sponsor: University of California System wide Biotechnology Research and Education Program, Grant sponsor: Institute for Genomics and Bioinformatics at UCI.

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