Tag: Protein Sequence

SimTandem 1.1.96 – Protein Sequence Identification

SimTandem 1.1.96

:: DESCRIPTION

SimTandem is a freely available tool for identification of peptides from LC-MS/MS spectra. It is based on a similarity search of mass spectra in a database of theoretical spectra generated from a database of known protein sequences.

::DEVELOPER

SIRET Research Group

:: SCREENSHOTS

SimTandem

:: REQUIREMENTS

  • Windows/Linux
  • OpenMS

:: DOWNLOAD

 SimTandem

:: MORE INFORMATION

Citation:

Jiri Novak, Timo Sachsenberg, David Hoksza, Tomas Skopal and Oliver Kohlbacher.
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications.
Journal of Integrative Bioinformatics, 10(3):228, 2013.

Epitopia – Detection of Immunogenic Regions in Protein Sequences

Epitopia

:: DESCRIPTION

 Epitopia is a server for detection of immunogenic regions in protein structures or sequences.Epitopia implements a machine learning scheme to rank individual amino acids in the protein, according to their potential of eliciting a humoral immune response.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Epitopia

:: MORE INFORMATION

Citation

Epitopia: a web-server for predicting B-cell epitopes.
Rubinstein ND, Mayrose I, Martz E, Pupko T.
BMC Bioinformatics. 2009 Sep 14;10:287. doi: 10.1186/1471-2105-10-287.

MUTPATH – Map Mutational Paths through Protein Sequence Space

MUTPATH

:: DESCRIPTION

mutpath is a Python package for identifying mutational paths through sequence space generated using the MarkovJumps feature of BEAST.

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 mutpath

:: MORE INFORMATION

Citation

L. Ian Gong and Jesse D. Bloom.
“Epistatically interacting substitutions are enriched during adaptive protein evolution.”
PLoS Genetics. 10:e1004328 (2014)

NetCTL 1.2b – Predict CTL Epitopes in Protein Sequence

NetCTL 1.2b

:: DESCRIPTION

NetCTL predicts CTL epitopes in protein sequences. NetCTL expands the MHC class I binding predicition to 12 MHC supertypes including the supertypes A26 and B39. The accuracy of the MHC class I peptide binding affinity is significantly improved compared to the earlier version. Also the prediction of proteasonal cleavage has been improved and is now identical to the predictions obtained by the NetChop-3.0 server. The updated version has been trained on a set of 886 known MHC class I ligands.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetCTL

:: MORE INFORMATION

Citation

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M.
BMC Bioinformatics. Oct 31;8:424. 2007

Gibbs Motif Sampler 3.2 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences

Gibbs Motif Sampler 3.2

:: DESCRIPTION

The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.

::DEVELOPER

Wadsworth Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows with Cygwin/MacOsX

:: DOWNLOAD

 Gibbs Motif Sampler

:: MORE INFORMATION

Citation

Neuwald AF, Liu JS, and Lawrence CE. (1995)
Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
Protein Sci 4(8):1618-1632. PubMed: 8520488.

Concavity 0.1 – Ligand Binding Site Prediction from Protein Sequence and Structure

Concavity 0.1

:: DESCRIPTION

Concavity predicts ligand-binding sites from structure.

::DEVELOPER

John A. Capra , Thomas Funkhouser , Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 Concavity

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000585. doi: 10.1371/journal.pcbi.1000585. Epub 2009 Dec 4.
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA1, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.

EFI-EST – Generating Protein Sequence Similarity Networks

EFI-EST

:: DESCRIPTION

EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool  is available without cost for the automated generation of protein sequence similarity networks.

::DEVELOPER

EFI-EST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL.
Biochim Biophys Acta. 2015 Apr 18. pii: S1570-9639(15)00112-0. doi: 10.1016/j.bbapap.2015.04.015.

RES – Scan Protein Sequence for its Repeatability

RES

:: DESCRIPTION

The RES (REpeatability Scanner) tool allows you to detect the repeatability of an input sequence. It shows how far from a perfect repeat is a sequence. Results will be automatically generated below the parameter selection.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

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