:: DESCRIPTION
ICeE is a database with a Web-browser interface that allows you to enter experiments for the nematode C. elegans and to search efficiently in this database.
::DEVELOPER
the Ewbank lab
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
visPIG is a web application to produce multi-track, multi-scale, multi-region plots of genetic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
visPIG–a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.
Scales M, Jäger R, Migliorini G, Houlston RS, Henrion MY.
PLoS One. 2014 Sep 10;9(9):e107497. doi: 10.1371/journal.pone.0107497. eCollection 2014.
:: DESCRIPTION
SketchBio is a tool that incorporates state-of-the-art bimanual interaction and drop shadowsto enable rapid construction of molecular structures and animations
::DEVELOPER
CISMM (Computer Integrated Systems for Microscopy and Manipulation)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 Oct 30;15(1):334.
SketchBio: a scientist’s 3D interface for molecular modeling and animation.
Waldon SM, Thompson PM, Hahn PJ, Taylor RM 2nd.
:: DESCRIPTION
ELASPIC constructs homology models of domains and domain-domain interactions, and uses those models, together with sequential and other features, to predict the energetic impact of a mutation on the stability of a single domain or the affinity between two domains.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ELASPIC web-server: proteome-wide structure based prediction of mutation effects on protein stability and binding affinity.
Witvliet D, Strokach A, Giraldo-Forero AF, Teyra J, Colak R, Kim PM.
Bioinformatics. 2016 Jan 21. pii: btw031.
:: DESCRIPTION
RamiGO is an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape.
::DEVELOPER
Princess Margaret Bioinformatics and Computational Genomics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Mar 1;29(5):666-8. doi: 10.1093/bioinformatics/bts708. Epub 2013 Jan 6.
RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.
Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.
:: DESCRIPTION
PDIviz is a plugin for the PyMOL molecular visualization system that is specifically designed to visualize protein-DNA interfaces in three dimensions. PDIviz detects the interface of protein-DNA complexes by calculating the buried surface area directly in PyMOL.
::DEVELOPER
MBL – Laboratorio de Bioinformática
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2015 Apr 16. pii: btv203.
PDIviz: Analysis and visualization of protein-DNA binding interfaces.
Ribeiro J, Melo F, Schüller A
:: DESCRIPTION
CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2011 Mar 25;6(3):e17695. doi: 10.1371/journal.pone.0017695.
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
de Vries SJ1, Bonvin AM.
:: DESCRIPTION
MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.
:: DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gabdoulline,R.R., Wade,R.C. and Walter,D.
MolSurfer: a macromolecular interface navigator
Nucl.Acid.Res. (2003) 31, 3349-3351.
:: DESCRIPTION
MADIBA is a web interface for functional analysis of cluster of genes with same profile of expression for Plasmodium falciparum, Oryza Sativa (rice), Arabidopsis thaliana and Pectobacterium atrosepticum
::DEVELOPER
the Bioinformatics and Computational Biology Unit at the University of Pretoria
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Law PJ, Claudel-Renard C, Joubert F, Louw AI and Berger DK (2008)
MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters
BMC Genomics 9:105
:: DESCRIPTION
PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables a user to create custom molecular modeling algorithms with Rosetta sampling and scoring functions using Python scripting. PyRosetta is designed to make the sophisticated Rosetta molecular modeling suite accessible to a broader audience of scientists in the life sciences.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Chaudhury, S. Lyskov & J. J. Gray,
“PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta,”
Bioinformatics, 26(5), 689-691 (2010).
