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SCALOP specifications

Information


Unique identifier OMICS_32532
Name SCALOP
Alternative name Sequence-based antibody CAnonical LOoP structure annotation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of amino acid sequences of full antibody chains.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
HMMER
Registration required Yes
Maintained No

Versioning


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Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_32532
Name SCALOP
Alternative name Sequence-based antibody CAnonical LOoP structure annotation
Interface Web user interface
Restrictions to use None
Input data A set of amino acid sequences of full antibody chains.
Input format FASTA
Programming languages Python
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for Sequence-based antibody CAnonical LOoP structure annotation

SCALOP citations

 (17)
library_books

Challenges for Quality Assurance of Target Volume Delineation in Clinical Trials

2017
PMCID: 5622143
PMID: 28993798
DOI: 10.3389/fonc.2017.00221

[…] had major inconsistencies in EBRT contouring. Centers with experience in IGBT (>30 cases) performed better than those with limited experience.Retrospective individual case review was reported by the SCALOP trial in pancreatic cancer (). The chief investigator and a radiologist contoured the GTV on the 60 of 74 patients who received radiotherapy in the study (12 patients had planning CTs which wer […]

library_books

Pancreatic Ductal Adenocarcinoma: Current and Evolving Therapies

2017
Int J Mol Sci
PMCID: 5535831
PMID: 28640192
DOI: 10.3390/ijms18071338

[…] d restricted to good PS patients. Moreover, capecitabine’s superiority over gemcitabine as a radiosensitiser has been proposed in the selective chemoradiation in advanced localised pancreatic cancer (SCALOP) trial []. Other studies investigating combination therapy with gemcitabine showed very moderate or no significant improvement. Therapy using gemcitabine and platinum analogues (cisplatin or ox […]

library_books

Correlation of 18F Fluorodeoxyglucose Positron Emission Tomography Parameters with Patterns of Disease Progression in Locally Advanced Pancreatic Cancer after Definitive Chemoradiotherapy

2017
PMCID: 5429392
PMID: 28190636
DOI: 10.1016/j.clon.2017.01.038

[…] ng were excluded, only 17 patients were able to be included in this analysis. FDG-PET staging and response assessment is not currently routine in LAPC. Patients recruited to recently published series SCALOP and LAP07 did not routinely have FDG-PET studies , . All of our observations and recommendations are therefore presented with a degree of caution as they are drawn from such a small sample.The […]

library_books

Modelling duodenum radiotherapy toxicity using cohort dose volume histogram data

2017
PMCID: 5486774
PMID: 28600084
DOI: 10.1016/j.radonc.2017.04.024

[…] intended to supplement the available published reports through access to individual patient data from two prospective clinical trials of chemoradiotherapy for locally-advanced pancreatic cancer: the SCALOP study (NCT 01032057, n = 74) in which patients were randomised to receive either gemcitabine or capecitabine , and the ARCII study (EudraCT 2008-006302-42, n = 23) in which patients received co […]

library_books

Long term results and recurrence patterns from SCALOP: a phase II randomised trial of gemcitabine or capecitabine based chemoradiation for locally advanced pancreatic cancer

2017
Br J Cancer
PMCID: 5482737
PMID: 28376080
DOI: 10.1038/bjc.2017.95

[…] %, specificity=64.3% ). Proportional change in CA19.9 between baseline and week 17 was less able to predict 12-month OS (area under ROC curve=0.6505, graph not shown).Of the 74 patients randomised in SCALOP, 2 patients progressed prior to the start of radiotherapy leaving 72 patients in the per protocol analysis. CA19.9 at week 17 was missing in 14 patients, tumour volume measurement was missing i […]

library_books

Consensus guidelines for diagnosis, treatment and follow up of patients with pancreatic cancer in Spain

2016
PMCID: 5427095
PMID: 27995549
DOI: 10.1007/s12094-016-1594-x

[…] al beam radiation and gemcitabine-based chemotherapy and the results cannot be extrapolated to those obtained with new chemotherapy regimens and more modern radiation techniques (IMRT). Data from the SCALOP trial (Phase II study of induction chemotherapy followed by GEM or capecitabine-based chemoradiation in locally advanced pancreatic cancer) suggest that the radiotherapy combined with fluoropyr […]


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SCALOP institution(s)
Department of Statistics, University of Oxford, Oxford, UK; Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany; UCB Pharma, Slough, UK; Computational and Modelling Sciences, GlaxoSmithKline Research and Development, Stevenage, UK; Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
SCALOP funding source(s)
Supported by funding from the EPSRC and MRC [grant number EP/L016044/1].

SCALOP review

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Desktop
The cluster information in the output is not very useful in antibody CDR template selection for modelling. This tool is suitable for High-throughput sequence analysis.