STITCH 5.0 – Search Tool for Interactions of Chemicals and proteins

STITCH 5.0

:: DESCRIPTION

STITCH (search tool for interactions of chemicals)  is a resource to explore known and predicted interactions of chemicals and proteins.Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

 STITCH

:: MORE INFORMATION

Citation

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.
Nucleic Acids Res. 2015 Nov 20. pii: gkv1277.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M1, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

STITCH: interaction networks of chemicals and proteins.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P
Nucleic Acids Res. 2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.

ChemiRs – Web Server for microRNAs and Chemicals

ChemiRs

:: DESCRIPTION

ChemiRs is a creditable online web server for predicting interactions and relations among miRNAs, chemicals and pathways.

::DEVELOPER

NTNU BISBE

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChemiRs: a web application for microRNAs and chemicals.
Su EC, Chen YS, Tien YC, Liu J, Ho BC, Yu SL, Singh S.
BMC Bioinformatics. 2016 Apr 18;17(1):167. doi: 10.1186/s12859-016-1002-0.

CheNER v2 – Chemical Named Entity Recognizer

CheNER v2

:: DESCRIPTION

CheNER is a named entity recognition tool, that uses Conditional Random Fields for identifying mentions of chemicals in text, focusing on IUPAC entities.

::DEVELOPER

the Structural Computational Biology Group at CNIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • JRE

:: DOWNLOAD

 CheNER

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1039-40. doi: 10.1093/bioinformatics/btt639. Epub 2013 Nov 13.
CheNER: chemical named entity recognizer.
Usié A1, Alves R, Solsona F, Vázquez M, Valencia A.

Chem3D for iPad 2.0.2 – View and manipulate stunning 3D chemical and biochemical images

 Chem3D for iPad 2.0.2

:: DESCRIPTION

Chem3D® for iPad is a free, structurally accurate molecular viewer for exploring and interacting with 3D models. Chem3D® can import 3D models with a wide variety of structural file types, and models can be rotated and scaled with the touch of finger to expose different viewpoints.

::DEVELOPER

PerkinElmer

:: SCREENSHOTS

Chem3D

:: REQUIREMENTS

  • iPad

:: DOWNLOAD

 Chem3D for iPad

:: MORE INFORMATION

Benchware® 3D Explorer 2.7 – 3D Chemical Visualization

Benchware® 3D Explorer 2.7

:: DESCRIPTION

Benchware® 3D Explorer has been designed specifically to make interacting with, learning from, and experimenting on, 3D chemical structures fit into research workflows and provides the means for any life science researcher to make more informed decisions by employing 3D molecular visualization on their desktop PC.

::DEVELOPER

Tripos, L.P.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Benchware® 3D Explorer

:: MORE INFORMATION

MapFold – Predicting Secondary Structure of RNA using Chemical and Enzymatic Mapping data

MapFold

:: DESCRIPTION

MapFold is a tool for predicting secondary structure of RNA using chemical and enzymatic mapping data. It is designed to take as input a combination of sequence and chemical probing data, and as output returns structures from the ensemble that are the closest match to the structural details contained within the probing data.

::DEVELOPER

The Laederach Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNA. 2010 Jun;16(6):1108-17. doi: 10.1261/rna.1988510. Epub 2010 Apr 22.
Evaluation of the information content of RNA structure mapping data for secondary structure prediction.
Quarrier S, Martin JS, Davis-Neulander L, Beauregard A, Laederach A.

GCAligner 1.0 – Alignment of Chemical data obtained by Gas Chromatography

GCAligner 1.0

:: DESCRIPTION

GCAligner  is a software designed to perform a preliminary alignment of chemical data obtained by gas chromatography. It was created to facilitate the comparison of multiple samples. The alignment algorithm is based on the comparison between each retention time, the following retention time in the same sample and its closest retention times in other samples. GCAligner is a java executable software running on any operating system. The input data file and the single output file containing the align data set are text files with tab delimited pieces of information.
See the software manual for further details.

::DEVELOPER

Simon Dellicour and Thomas Lecocq @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

   GCAligner

:: MORE INFORMATION

PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter

PovChem 2.1.1

:: DESCRIPTION

PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration – colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds.

PovChem can export the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything!

::DEVELOPER

Paul A. Thiessen

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PovChem

:: MORE INFORMATION

PovChem is now free!Use this key to register your copy of PovChem:
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