:: DESCRIPTION
SPuNC (Structure Prediction using Nucleotide Composition) provides a method for RNA structure prediction using evolutionary patterns of nucleotide composition.
::DEVELOPER
The Centre for Integrative Bioinformatics VU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sandra Smit, Rob Knight, and Jaap Heringa
RNA structure prediction from evolutionary patterns of nucleotide composition.
NAR (2009) 37(5):1378-86
:: DESCRIPTION
DisEMBL is a protein disorder prediction software based on neural networks. Predicts propensity for loops (no helix, no strand), hot loops (floppy loops with high temperature factors), and disordered regions (called “Remark465” in DISEMBL).
::DEVELOPER
Rune Linding & Lars Juhl Jensen – EMBL
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell
Protein disorder prediction: implications for structural proteomics
Structure Vol 11, Issue 11, 4 November 2003
:: DESCRIPTION
InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe Aude, Pierre Legrain and Henning Hermjakob,
InteroPORC: Automated Inference of Highly Conserved Protein Interaction Networks
Bioinformatics, 24(14): 1625-1631
:: DESCRIPTION
NOXclass is a classifier identifying protein-protein interaction types (biological obligate, biological non-obligate and crystal packing) implemented using a support vector machine (SVM) algorithm. NOXclass allows the interpretation and analysis of protein quaternary structures. In particular, it generates testable hypotheses regarding the nature of protein-protein interactions, when experimental results are not available.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hongbo Z, Domingues FS, Sommer I and Lengauer T.
NOXclass: prediction of protein-protein interaction types.
(2006). BMC Bioinformatics 2006, 7:27
:: DESCRIPTION
CDPred (Conserved Domain-based Prediction) is a computational algorithm that is designed to theoretically calculate the effect of substituting an amino acid relative to the reference sequence within functional modules – the protein domains. Effectively, CDPred computes the deviation (as reported by delta-score) from the expected in a position-specific manner, based on domain annotations in the NCBI Conserved Domain Database (CDD). So this method was designed to analyze the missense variation and mutations in humans (though can be used for any organism) in the light of conservation within functional units of the protein. Lower the value of delta-score (more negative the score), more severe or deleterious the predicted effect on the function of the protein. We set 0 to -3 as mild / neutral effects, -4 to -6 as medium effects, and -7 and lower as severe effects. A severity score of -30 is assigned to termination or stop changes, as they would lead to a truncated protein product. It must be noted that positive scores above 3 (high positive-scores) may also be potentially damaging, but a strongly positive score generally results from a situation where the normal human amino acid at a position is different from many or all other aligned species over a domain, and that the variant allele is closer to the ancestral form. For example, if an individual had the ancestral form of the FOXP2 gene, that individual would potentially exhibit loss of speech, however, the delta score for the amino acid positions that are unique to all other humans would be positive because that individual more closely resembles the ancestral form.
:DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Johnston, J.J., Teer, J.K., Cherukuri, P.F., Hansen, N.F., Loftus, S.K., NIH Intramural Sequencing Center, Chong, K., Mullikin, J.C., Biesecker, L.G. 2010.
Massively parallel sequencing of exons on the X chromosome identify RBM10 as the gene that causes a syndromic form of cleft palate.
Am J Hum Genet. 2010 May 14;86(5):743-8.
:: DESCRIPTION
ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework.
::DEVELOPER
Institut für Informatik, Ludwig-Maximilians-Universität München
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer.
ProCope–protein complex prediction and evaluation.
Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 2008.
:: DESCRIPTION
HMMSTR-CM is a software for protein contact map predictions. As above a sequence profile is the input. HMMSTR-CM gives you a JPEG image and text file showing the residues that are most likely to come into contact (distance < 8.0A) in the folded structure. This too is a bare-bones package. This script runs as part of the HMMSTR/Rosetta server.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citaiton
Shao Y & Bystroff C. (2003a).
Predicting inter-residue contacts using templates and pathways.
Proteins, Structure, Function and Genetics 53 Suppl 6:497-502.
