RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination

RDC-PANDA 1.0

:: DESCRIPTION

RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

RDC-PANDA

:: MORE INFORMATION

Citation

Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Journal of Biomolecular NMR, 45(3):265-281, 2009

MPtopoQuerier – Search Database of Membrane Proteins

MPtopoQuerier

:: DESCRIPTION

MPtopoQuerier is a java applet developed for searching MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool.

::DEVELOPER

Stephen White laboratory at UC Irvine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

MPtopoQuerier

:: MORE INFORMATION

Citation

Jayasinghe, S., Hristova, K., and White, S. H. (2001).
MPtopo: A database of membrane protein topology.
Protein Sci 10:455-458.

MPEx 3.2 – Tool for Exploring Membrane Proteins

MPEx 3.2

:: DESCRIPTION

MPEx (Membrane Protein Explorer) is a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles.

::DEVELOPER

Stephen White laboratory at UC Irvine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

MPEx

:: MORE INFORMATION

Citation

Snider C, Jayasinghe S, Hristova K, & White SH (2009).
MPEx: A tool for exploring membrane proteins.
Protein Sci 18:2624-2628. [PubMed Abstract].

Ebbie 3.0.9 – Analysis & Storage of Small RNA Cloning Data

Ebbie 3.0.9

:: DESCRIPTION

Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases.

::DEVELOPER

H Alexander Ebhardt

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Ebbie

:: MORE INFORMATION

Citation

H Alexander Ebhardt , Kay C Wiese and Peter J Unrau
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
BMC Bioinformatics 2006, 7:185doi:10.1186/1471-2105-7-185

Ebbie-MM 4.3 – Analyze Single Mismatches of Small RNAs to the genome

Ebbie-MM 4.3

:: DESCRIPTION

Ebbie-MM (Ebbie-(mis)match) is a software that analyzes single mismatches of small RNAs to the genome of origin. Using Ebbie-MM, we analyzed a dataset of 7,790 non-redundant small RNAs cloned from Oryza sativa. In this limited dataset, we found 230 1-nt-mismatches of which only 19 % overlapped to themselves. Even with this very limited dataset of 43 overlapping 1-nt-mismatches, RNA base modifications were detectable in small RNAs. Thus, not all sequencing errors should be discarded as they could contain valuable information on RNA base modifications.

::DEVELOPER

H Alexander Ebhardt , Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java
  • NCBI-Blast

:: DOWNLOAD

Ebbie-MM

:: MORE INFORMATION

Citation

H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bosta3 and Richard P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucl. Acids Res. (2009) 37 (8): 2461-2470

RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure

RNA-DV 1.0

:: DESCRIPTION

RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).

::DEVELOPER

Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNA-DV

:: MORE INFORMATION

FSFinder 2.0 – Predict Frameshifting in Genomic Sequences

FSFinder 2.0

:: DESCRIPTION

FSFinder (Frameshift Signal Finder) is a software that searches the genomic sequences or mRNA sequences for frameshifting sites.FSFinder is capable of finding -1 frameshift sites for most known genes and +1 frameshift sites for two genes: protein chain release factor (prfB ) and ornithine decarboxylase antizyme (oaz ).

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

FSFinder

:: MORE INFORMATION

Citation

Byun Y, Moon S, Han K.
A general computational model for predicting ribosomal frameshifts in genome sequences.
Comput Biol Med. 2007 Dec;37(12):1796-801. Epub 2007 Aug 2.

PRI-Modeler 1.3 – Extract RNA Structure elements from PDB files of Protein-RNA Complexes

PRI-Modeler 1.3

:: DESCRIPTION

PRI-Modeler (protein-RNA interaction modeler)analyzes the conformation of the RNA, calculates the hydrogen bond (H bond) and van der Waals interactions between amino acids and nucleotides, extracts secondary and tertiary RNA structure elements, and identifies the patterns of interactions between the proteins and RNAs. This paper presents PRI-Modeler and its application to the hydrogen bond and van der Waals interactions in the most representative set of protein-RNA complexes. The analysis reveals several interesting interaction patterns at various levels.

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PRI-Modeler

:: MORE INFORMATION

Citation

Kyungsook Han, Chirag Nepa
PRI-Modeler: Extracting RNA structural elements from PDB files of protein–RNA complexes
FEBS Lett. 2007 May 1;581(9):1881-90.

InterViewer 4.0 – Visualize Large-scale Protein Interaction Networks

InterViewer 4.0

:: DESCRIPTION

InterViewer is a software for visualizing large-scale protein interaction networks. InterViewer  (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

InterViewer

:: MORE INFORMATION

Citation

Byong-Hyon Ju, Byungkyu Park, Jong H. Park and Kyungsook Han
Visualization and analysis of protein interactions
Bioinformatics (2003) 19 (2): 317-318.

PseudoViewer 3.0 – Visualization of RNA Pseudoknots of any type

PseudoViewer 3.0

:: DESCRIPTION

PseudoViewer is a program for visualizing RNA secondary structures with pseudoknots. Experimental results show that the PseudoViewer web service and web application are useful for resolving many problems with incompatible software components as well as for visualizing large-scale RNA secondary structures with pseudoknots of any type.

PseudoViewer Online Version

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PseudoViewer

:: MORE INFORMATION

Citation

Y. Byun and K. Han,
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots,
Bioinformatics, Vol. 25, 1435-1437, 2009.