CanProVar 2.0 – Human Cancer Proteome Variation Database

CanProVar 2.0

:: DESCRIPTION

CanProVar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.
Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B, Li Y, Li J.
J Proteome Res. 2017 Feb 3;16(2):421-432. doi: 10.1021/acs.jproteome.6b00505.

mutation3D 201512 – Find Clusters of Cancer-causing Mutations in the human Proteome

mutation3D 201512

:: DESCRIPTION

mutation3D is a functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures.

::DEVELOPER

Yu Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 mutation3D

:: MORE INFORMATION

M2Lite 20150127 – Proteome Discoverer MSF to mzIdentML Tool

M2Lite 20150127

:: DESCRIPTION

M2Lite is a lightweight, easily pluggable, and extremely fast conversion software tool. M2Lite converts msf files to the proteomics community standard mzIdentML file format.

::DEVELOPER

Paul Aiyetan

:: SCREENSHOTS

NIHMS614474.html

:: REQUIREMENTS

  • Linux / Windows
  • JDK
  • R

:: DOWNLOAD

 M2Lite

:: MORE INFORMATION

Citation:

J Bioinform. 2014 Apr 28;1(2):40-49.
M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.
Aiyetan P, Zhang B, Chen L, Zhang Z, Zhang H

GlycoMine – Predicting N-, C- and O-linked glycosylation in the Human Proteome

GlycoMine

:: DESCRIPTION

GlycoMine is a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

::DEVELOPER

Jiangning Song, Ph.D.

:: SCREENSHOTS

GlycoMine

:: REQUIREMENTS

  • Linux/MacOsX/ Windows
  • Java

:: DOWNLOAD

 GlycoMine

:: MORE INFORMATION

Citation:

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.
Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J.
Bioinformatics. 2015 Jan 6. pii: btu852.

ProteinART – Protein Inference solutions from Proteome ARTworks

ProteinART

:: DESCRIPTION

ProteinART is a web tool that uses combinatorial optimization for protein inference from tandem mass spectrometry peptide identifications. It uses a set of confidently identified peptides, peptide detectability, and a protein database to provide the most likely set of identified proteins.

::DEVELOPER

Haixu Tang, Predrag Radivojac

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2007:409-20.
Advancement in protein inference from shotgun proteomics using peptide detectability.
Alves P1, Arnold RJ, Novotny MV, Radivojac P, Reilly JP, Tang H.

Tardigrade Analyzer 2.00 – Tardigrade (Waterbear) Genome and Proteome Analysis

Tardigrade Analyzer 2.00

:: DESCRIPTION

Tardigrade Analyzer offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data.

::DEVELOPER

the Department of Bioinformatics at the University of Würzburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Oct 12;10:469. doi: 10.1186/1471-2164-10-469.
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.
Förster F, Liang C, Shkumatov A, Beisser D, Engelmann JC, Schn?lzer M, Frohme M, Müller T, Schill RO, Dandekar T.

FCP – Functional Coverage of the Proteome by Structures

FCP

:: DESCRIPTION

 FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes (specially kinases and proteases), G protein-coupled receptors, nuclear receptors and transporters/channels, offering both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures, as well as on the bias observed in the distribution of those structures among proteins.

::DEVELOPER

The Chemogenomics Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

FCP: functional coverage of the proteome by structures.
García-Serna R, Opatowski L, Mestres J.
Bioinformatics. 2006 Jul 15;22(14):1792-3. Epub 2006 May 16.