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Protocols

SCORER specifications

Information


Unique identifier OMICS_07847
Name SCORER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Thomas L. Vincent

Information


Unique identifier OMICS_07847
Name SCORER
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Thomas L. Vincent

Publications for SCORER

SCORER citations

 (5)
call_split

PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection

2018
Genes
PMCID: 5852587
PMID: 29443925
DOI: 10.3390/genes9020091
call_split See protocol

[…] ex structure database, to create and verify the prediction system. One of the datasets was CC + DATABASE [], which Testa et al. proposed after adjusting the coiled-coil structure and polymer data. In SCORER 2.0 web server, they also utilized the CC + DATABASE but only the parallel dimer and trimer coiled-coil data. In the present study, we used the dataset of all polymers in the CC + DATABASE and […]

library_books

The Plasmodium Class XIV Myosin, MyoB, Has a Distinct Subcellular Location in Invasive and Motile Stages of the Malaria Parasite and an Unusual Light Chain*

2015
PMCID: 4424349
PMID: 25802338
DOI: 10.1074/jbc.M115.637694

[…] tic tree construction was performed using CLC Sequence Viewer 6, using the neighbor joining method () and 100 replicates for bootstrap analysis. Coiled-coil prediction was performed using MARCOIL and Scorer 2.0 (, ). A structural model of PfMLC-B calmodulin (CaM)-like domain (amino acids 508–645) was constructed using Phyre 2 protein fold recognition server (). Amino acids 508–645 were modeled on […]

library_books

Mechanism of the Rpn13 induced activation of Uch37

2014
PMCID: 4130924
PMID: 24752541
DOI: 10.1007/s13238-014-0046-z

[…] rm a coiled-coil motif, which has been implicated in protein-protein interactions, particularly in the formation of multimeric complexes and molecular recognition (Zhang et al., ; Larzabal et al., ). SCORER 2.0 software identified that Hc formed perfect coiled-coil motifs (Armstrong et al., ). As predicted, four Hc helices interacted with each other mainly through hydrophobic residues, such as F29 […]

library_books

Resistome analysis of Mycobacterium tuberculosis: Identification of aminoglycoside 2' Nacetyltransferase (AAC) as co target for drug desigining

2013
Bioinformation
PMCID: 3602886
PMID: 23519100
DOI: 10.6026/97320630009174

[…] ysis of representative AAC from each clad of the phylogenic tree provides very important informatics about the basic ancestral core of all different AAC from M. tuberculosis and related species. From SCORER 2.0, analysis all AAC was predicted to form dimer and MEME analysis shows that region which is involved in dimer formation is conserved for all structures. Another important result from MEME an […]

library_books

Collagen Like Proteins in Pathogenic E. coli Strains

2012
PLoS One
PMCID: 3368898
PMID: 22701585
DOI: 10.1371/journal.pone.0037872

[…] fam databases (). The probability of coiled-coil conformation and its oligomerization state in EPclP sequences were calculated with different prediction algorithms: PCoils , Marcoil , MultiCoil and SCORER 2.0 . Secondary structure predictions for EPclP sequences were obtained from the Jpred3 prediction server . Default settings were used for all prediction algorithms. […]

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SCORER institution(s)
School of Chemistry, University of Bristol, Bristol, UK

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