Tag: Domain

Cytoprophet 1.0 – A Cytoscape plug-in for Protein and Domain Interaction Networks Inference

Cytoprophet 1.0

:: DESCRIPTION

Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.

::DEVELOPER

Cytoprophet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Cytoprophet

:: MORE INFORMATION

Citation

Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007

DASH 1.0 – Domain Analysis of Symbionts and Hosts

DASH 1.0

:: DESCRIPTION

DASH  determines for a pathogen, domains within its genes, and the host genes sharing those domains.

::DEVELOPER

Spouge Research Group

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 May 24;6:209. doi: 10.1186/1756-0500-6-209.
Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses.
Gonzalez MW1, Spouge JL.

loctree3 – Protein Sub-cellular Localization Prediction for all Domains of Life

LocTree3

:: DESCRIPTION

LocTree3 that predicts localization for all proteins in all domains of life. We incorporate a system of hierarchically organized Support Vector Machines to mimic the protein trafficking mechanism in cells.

::DEVELOPER

the Rostlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  LocTree3

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W350-5. doi: 10.1093/nar/gku396.
LocTree3 prediction of localization.
Goldberg T et cl.

DODO – DOmain based Detection of Orthologs

DODO

:: DESCRIPTION

DODO is an efficient method to detect orthologs in genomes. Given protein sequences of interested genomes, DODO can identify orthologous relationship based on protein domain information.

::DEVELOPER

Transcriptome Discovery Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DODO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S6. doi: 10.1186/1471-2105-11-S7-S6.
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.
Chen TW1, Wu TH, Ng WV, Lin WC.

Protein Peeling 3D – Splitting Protein Structure into Proteins Units and Domains

Protein Peeling 3D

:: DESCRIPTION

Protein Peeling 3D web server dedicated to the analysis of protein structure architecture through the identification of protein units produced by an iterative splitting algorithm.

::DEVELOPER

Protein Peeling 3D team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Protein Peeling 3D: new tools for analyzing protein structures.
Gelly JC, de Brevern AG.
Bioinformatics. 2011 Jan 1;27(1):132-3. doi: 10.1093/bioinformatics/btq610.

DANTE – Domain based ANnotation of Transposable Elements

DANTE

:: DESCRIPTION

DANTE uses database of Viridiplantae protein domains derived from transposable elements omains searching is accomplished engaging LASTAL alignment tool.

::DEVELOPER

Laboratory of Molecular Cytogenetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DANTE

:: MORE INFORMATION

DOMIRE – DOMain Identification from Recurrence

DOMIRE

:: DESCRIPTION

DOMIRE is a program using VAST to define the domain boundaries in proteins from their 3D structures with a list of structural neighbours.

::DEVELOPER

DOMIRE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DOMIRE: a web server for identifying structural domains and their neighbors in proteins.
Samson F, Shrager R, Tai CH, Sam V, Lee B, Munson PJ, Gibrat JF, Garnier J.
Bioinformatics. 2012 Apr 1;28(7):1040-1. doi: 10.1093/bioinformatics/bts076.

SMART 8.0 – Analysis of Protein Domain Architectures

SMART 8.0

:: DESCRIPTION

SMART (Simple Modular Architecture Research Tool) is an online resource for the identification and annotation of protein domains and the analysis of protein domain architectures.More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Letunic I, Doerks T, Bork P
SMART: recent updates, new developments and status in 2015
Nucleic Acids Res 2014; doi:10.1093/nar/gku949

Letunic et al. (2012)
SMART 7: recent updates to the protein domain annotation resource
Nucleic Acids Res , doi:10.1093/nar/gkr931

RCDP – Performs Co-evolutionary Analysis of Domains in Interacting Proteins to Predict Domain Pair(s)

RCDP

:: DESCRIPTION

RCDP (Relative Co-evolution of Domain Pairs) tests the generality of the observed behavior, and to predict large-scale domain–domain interactions using the yeast inter-actome.

::DEVELOPER

Teresa Przytycka Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • perl 

:: DOWNLOAD

 RCDP

:: MORE INFORMATION

Citation

Raja Jothi et al.
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
Journal of Molecular Biology, 29;362(4):861-75, 2006

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