Tag: Chemical

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

CheNER – Chemical Named Entity Recognizer

CheNER

:: 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.

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.

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.

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:
APyUrblJnYZr

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