:: DESCRIPTION
Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1-dev for HMM searching in DNA:DNA style
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
IDRBind is a protein interface predictor for binding sites of intrinsically disordered protein regions (IDRs), ranging from peptide motifs (i.e., short linear motifs) to molecular recognition features (MoRFs). Differentiating IDRBind from other interface predictors is its emphasis on binding sites of MoRFs, which are long interaction mediating elements within IDRs.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wong ETC, Gsponer J.
Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions.
J Mol Biol. 2019 Aug 9;431(17):3157-3178. doi: 10.1016/j.jmb.2019.06.010. Epub 2019 Jun 15. PMID: 31207240.
:: DESCRIPTION
Cis-regPred predicts intrinsically disordered protein regions that may regulate protein function by mediating interactions in cis.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yeon JH, Heinkel F, Sung M, Na D, Gsponer J.
Systems-wide Identification of cis-Regulatory Elements in Proteins.
Cell Syst. 2016 Feb 24;2(2):89-100. doi: 10.1016/j.cels.2016.02.004. Epub 2016 Feb 24. PMID: 27135163.
:: DESCRIPTION
DBSI (DNA Binding Site Identifier), is a binding site predictor for DNA, and it has also successfully identified binding sites for RNA and heparin.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DBSI Server: DNA Binding Site Identifier.
Sukumar S, Zhu X, Ericksen SS, Mitchell JC.
Bioinformatics. 2016 Jun 3. pii: btw315.
:: DESCRIPTION
MPRAP is a novel Membrane Protein Residue Accessibility Predictor, based on sequence derived information. In contrast to previous membrane predictors, MPRAP, performs well both within and outside the membrane regions and outperforms earlier methods in the membrane regions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Jun 18;11:333. doi: 10.1186/1471-2105-11-333.
MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane.
Illergård K1, Callegari S, Elofsson A.
:: DESCRIPTION
CELLO is a multi-class SVM classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. We combine votes from these classifiers and use the jury votes to determine the final assignment.
CELLO2GO is a publicly available, web-based system for screening various properties of a targeted protein and its subcellular localization.
::DEVELOPER
CELLO team, National Chiao Tung University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation.
Yu CS, Cheng CW, Su WC, Chang KC, Huang SW, Hwang JK, Lu CH.
PLoS One. 2014 Jun 9;9(6):e99368. doi: 10.1371/journal.pone.0099368.
Protein Sci. 2004 May;13(5):1402-6.
Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions.
Yu CS, Lin CJ, Hwang JK.
:: DESCRIPTION
ILbind is a consensus predictor that combines the two complementary inverse ligand binding predictors implemented using FINDSITE and SMAP and Support Vector Machines.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hu G, Gao J, Wang K, Mizianty MJ, Ruan J, Kurgan L.
Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions.
Bioinformatics. 2014 Aug 28. pii: btu581. [Epub ahead of print]
:: DESCRIPTION
iLocator is an image-based multi-label subcellular location predictor, which covers 7 cellular localizations, i.e. cytoplasm, endoplasmic reticulum, Golgi apparatus, lysosome, mitochondria, nucleus, and vesicles. The iLocator incorporates both global and local image descriptors, and uses an ensemble multi-label classifier to generate accurate predictions.
::DEVELOPER
Computational Systems Biology Group, Shanghai Jiao Tong University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Aug 15;29(16):2032-40. doi: 10.1093/bioinformatics/btt320. Epub 2013 Jun 4.
An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues.
Xu YY1, Yang F, Zhang Y, Shen HB.
:: DESCRIPTION
SOMRuler is a novel TMH predictor with excellent interpretability while possessing high prediction accuracy.
::DEVELOPER
Computational Systems Biology Group, Shanghai Jiao Tong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
IEEE Trans Nanobioscience. 2011 Jun;10(2):121-9. doi: 10.1109/TNB.2011.2160730. Epub 2011 Jul 7.
SOMRuler: a novel interpretable transmembrane helices predictor.
Yu D, Shen H, Yang J.
:: DESCRIPTION
GraPPLE are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.
::DEVELOPER
Max Planck Institute for Molecular Plant Physiology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.
