AS-EAST 1.1.3 – Annotate and Analyzes users’ uploaded Transcript data

AS-EAST 1.1.3

:: DESCRIPTION

AS-EAST (Alternative Splicing Effects ASsessment Tools) is an online tool for the functional annotation of putative proteins encoded by transcripts generated by alternative splicing (AS).

::DEVELOPER

Nagahama Institute of Bio-Science and Technology

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 1;28(15):2076-7. doi: 10.1093/bioinformatics/bts320.
AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts.
Shionyu M, Takahashi K, Go M.

LocNES – Locating Classical NESs in CRM1 Cargo Proteins

LocNES

:: DESCRIPTION

LocNES (Locating Nuclear Export Signals or NESs) is a Support Vector Machine (SVM) predictor that locates classical nuclear export signals (NESs) in CRM1 cargoes. Export-Karyopherinβ CRM1 recognizes hundreds of broadly functioning proteins. Most CRM1 cargoes contain the classical NES (also known as leucine-rich NESs), a peptide with 8-15 amino acids, regularly spaced with conserved hydrophobic residues.

::DEVELOPER

Chook Lab,UT Southwestern Medical Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

LocNES: A computational tool for locating classical NESs in CRM1 cargo proteins.
Xu D, Marquis K, Pei J, Fu SC, Cağatay T, Grishin NV, Chook YM.
Bioinformatics. 2014 Dec 15. pii: btu826.

DISOPRED 3.16 – Intrinsic Protein Disorder Prediction

DISOPRED 3.16

:: DESCRIPTION

DISOPRED is a SVM-based predictor of disordered regions in proteins.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Unix/MacOsX
  • any ANSI C and C++ compiler

:: DOWNLOAD

 DISOPRED

:: MORE INFORMATION

Citation

Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF and Jones DT (2004)
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
J. Mol. Biol., 337, 635-645.

MHC-NP – Prediction of Peptides Naturally Processed by the MHC

MHC-NP

:: DESCRIPTION

MHC-NP is a python tool to identify peptides that are naturally processed by the MHC-I pathway.

::DEVELOPER

Machine Learning Research Group at Laval University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sébastien Giguère, Alexandre Drouin, Alexandre Lacoste, Mario Marchand, Jacques Corbeil, and François Laviolette
MHC-NP: Predicting peptides naturally processed by the MHC.”
Journal of immunological methods 400 (2013): 30-36.

(PS)2 v3 – Protein Structure Prediction server

(PS)2 v3

:: DESCRIPTION

(PS)2 is an automated homology modeling server. The method uses an effective consensus strategy by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment. The final three dimensional structure is built using the modeling package MODELLER.

::DEVELOPER

(PS)2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

(PS)2: protein structure prediction server version 3.0.
Huang TT, Hwang JK, Chen CH, Chu CS, Lee CW, Chen CC.
Nucleic Acids Res. 2015 May 5. pii: gkv454.

Chen CC, Hwang JK, Yang JM.
(PS)2: protein structure prediction server.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W152-7.

Chen CC, Hwang JK, Yang JM:
(PS)2-v2: template-based protein structure prediction server.
BMC Bioinformatics 2009, 10:366

PREDDIMER – Prediction tool for an Ensemble of Transmembrane α-helical Dimer Conformations

PREDDIMER

:: DESCRIPTION

PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices.

::DEVELOPER

Laboratory of biomolecular modeling.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):889-90. doi: 10.1093/bioinformatics/btt645.
PREDDIMER: a web server for prediction of transmembrane helical dimers.
Polyansky AA1, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.

ASSIST v1- Active Site Similarity Search Tool

ASSIST v1

:: DESCRIPTION

ASSIST is an application for the detection of catalytic sites in unknown function proteins.

::DEVELOPER

the Theoretical Biology and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

  ASSIST

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1022-4. doi: 10.1093/bioinformatics/btt664. Epub 2013 Nov 15.
ASSIST: a fast versatile local structural comparison tool.
Caprari S, Toti D, Viet Hung L, Di Stefano M, Polticelli F.

NESmapper 1.1 – Prediction of CRM1-dependent Nuclear Export Signals

NESmapper 1.1

:: DESCRIPTION

NESmapper is a computational tool to predict nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions.

::DEVELOPER

NESmapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NESmapper

:: MORE INFORMATION

Citation

NESmapper: accurate prediction of leucine-rich nuclear export signals using activity-based profiles.
Kosugi S, Yanagawa H, Terauchi R, Tabata S.
PLoS Comput Biol. 2014 Sep 18;10(9):e1003841. doi: 10.1371/journal.pcbi.1003841.

BioAssemblyModeler (BAM) 2.1.0.2 – Homology Modeling of Protein Homo- and Heterooligomers

BAM 2.1.0.2

:: DESCRIPTION

BioAssemblyModeler (BAM) is a graphical user interface (GUI) application for building protein homooligomers and heterooligomers by means of comparative (homology) modeling.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BAM

:: MORE INFORMATION