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CCHMM_PROF specifications

Information


Unique identifier OMICS_07849
Name CCHMM_PROF
Interface Web user interface
Restrictions to use None
Input data Sequence
Input format Raw, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Piero Fariselli

Publication for CCHMM_PROF

CCHMM_PROF citations

 (4)
call_split

Identification of a homogenous structural basis for oligomerization by retroviral Rev like proteins

2017
Retrovirology
PMCID: 5568270
PMID: 28830558
DOI: 10.1186/s12977-017-0366-1
call_split See protocol

[…] io.dundee.ac.uk/jpred/index.html) []. JPred 3 provides a 3-state prediction (alpha-helix, beta-strand, other) with an accuracy of 81.5% []. Coiled-coil motif predictions were performed using both the CCHMM_PROF (http://gpcr.biocomp.unibo.it/cgi/predictors/cchmmprof/pred_cchmmprof.cgi) and COILS (http://www.ch.embnet.org/software/COILS_form.html) webservers [, ]. For CCHMM_PROF, default parameters […]

library_books

Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family

2017
Sci Rep
PMCID: 5533708
PMID: 28754924
DOI: 10.1038/s41598-017-05748-5

[…] uence alignment software and visualized with Jalview. Secondary structure was predicted using PSIPRED, whereas domains, repeats and other features were predicted with InterproScan. COILS, MARCOIL and CCHMM-PROF were used to assess previously predicted coiled-coil regions, and TPR modules were predicted with TPRpred. A repeat consensus was manually curated with Jalview from the MAFFT alignment. Fur […]

library_books

NUP 1 Is a Large Coiled Coil Nucleoskeletal Protein in Trypanosomes with Lamin Like Functions

2012
PLoS Biol
PMCID: 3313915
PMID: 22479148
DOI: 10.1371/journal.pbio.1001287

[…] NUP-1 is a large protein (pI 5.07, MW>400 kDa) associated with the nuclear periphery , that was identified as a major component of the T. brucei NE proteome . As predicted by both COILS and CCHMM_PROF, NUP-1 is almost exclusively coiled-coil with a central region of 17 near-perfect repeats of 144 amino acids () ,. No trans-membrane helices were predicted. Moreover, the N- and C-terminal […]

library_books

DISC1: Structure, Function, and Therapeutic Potential for Major Mental Illness

2011
PMCID: 3222219
PMID: 22116789
DOI: 10.1021/cn200062k

[…] structure within DISC1 was analyzed and annotated using coiled-coil predictors along with the secondary structure predictor, PsiPred.Depending on which program is used for detecting coiled-coils e.g. CCHMM_PROF, COILS, MarCoil, Multicoil, PairCoil2 () and PCOILS, the input provided (e.g., single sequence or multiple sequence alignment) and the stringency of the threshold parameters (e.g., use of a […]

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CCHMM_PROF institution(s)
Biocomputing Group, Department of Biology, University of Bologna, Bologna, Italy

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