:: DESCRIPTION
Pprint is a web-server for predicting RNA-binding residues of a protein.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Proteins. 2008 Apr;71(1):189-94.
Prediction of RNA binding sites in a protein using SVM and PSSM profile.
Kumar M1, Gromiha MM, Raghava GP.
:: DESCRIPTION
BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).
::DEVELOPER
The RNA-Informatics Research Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model.
Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.
Bioinformatics. 2015 Apr 16. pii: btv210.
:: DESCRIPTION
SPIDER is developed as a knowledge-based scoring function for protein-protein interaction decoys. SPIDER is a novel multi-body pose-scoring function that has no theoretical limit on the number of residues contributing to the individual interaction terms. SPIDER’s score relies on the geometric similarity of interfacial residues between docking poses and naturally occuring (native) poses.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raed Khashan, Weifan Zheng, and Alexander Tropsha.
Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.
Proteins: Structure, Function, and Bioinformatics, Volume 80, Issue 9, Pages 2207-2217, August 2012.
:: DESCRIPTION
PIANA (Protein Interactions And Network Analysis) is a software framework that facilitates the work with protein interaction networks by 1) integrating data from multiple sources in a centralized database, 2) providing a library that handles all operations related with the network and 3) automating the analysis of protein-protein interactions networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
R. Aragues, D. Jaeggi and B. Oliva
“PIANA: Protein Interactions and Network Analysis”
Bioinformatics. 2006 Apr 15;22(8):1015-7 (2006)
:: DESCRIPTION
TVi (“tree viewer with interactions”) is a tool for the visualisation of network data in the context of a phylogenetic tree.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BJ Holden, JW Pinney, SC Lovell, GD Amoutzias and DL Robertson
An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network (2007)
BMC Bioinformatics 8:289
:: DESCRIPTION
SISSI (Simulating Sequence Evolution with Site-Specific Interactions) is a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tanja Gesell and Arndt von Haeseler:
In silico sequence evolution with site-specific interactions along phylogenetic trees, Phylogenetic Trees.
Bioinformatics, 22:716-722, 2006.
:: DESCRIPTION
HapForest implements a forest-based approach to accommodate the haplotype uncertainties and variable importance to sort out significant haplotypes and their interactions in genomewide case-control association studies.
::DEVELOPER
The Collaborative Center for Statistics in Science(C2S2)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
X. Chen, C.-T. Liu, M. Zhang and H.P. Zhang.
A forest-based approach to identifying gene and gene-gene interactions,
PNAS, 104: 19199–19203, 2007.
:: DESCRIPTION
NUCPLOT is a program that automatically generates schematic 2D representations of protein-nucleic acid interactions. The input is a standard PDB file and the output is a colour or black-and-white PostScript file which gives a simple, at-a-glance representation of the hydrogen bonds and hydrophobic contacts between proteins and nucleic acids.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Luscombe N M, Laskowski R A, Thornton J M. (1997).
NUCPLOT: a program to generate schematic diagams of protein-DNA interactions.
Nucleic Acids Research, 25, 4940-4945.