GECS – Glycan Structure Prediction from Microarray data

GECS

:: DESCRIPTION

GECS (Gene Expression to Chemical Structure) is a collection of prediction methods linking genomic or transcriptomic contents of genes to chemical structures of biosynthetic substances. This N-Glycan Prediction Server is based on the repertoire of glycosyltransferases for N-glycan biosynthesis.

::DEVELOPER

Kyoto University Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Genome Inform. 2007;18:237-46.
An improved scoring scheme for predicting glycan structures from gene expression data.
Suga A, Yamanishi Y, Hashimoto K, Goto S, Kanehisa M.

RBO Aleph – Protein Contact and Structure Prediction Server

RBO Aleph

:: DESCRIPTION

RBO Aleph is a novel server for fully automated protein structure prediction. The server implements template-based modeling, protein contact prediction, and ab initio structure prediction.

::DEVELOPER

the Robotics and Biology Lab (RBO), Technische Universität Berlin.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RBO Aleph: leveraging novel information sources for protein structure prediction.
Mabrouk M, Putz I, Werner T, Schneider M, Neeb M, Bartels P, Brock O.
Nucleic Acids Res. 2015 Apr 20. pii: gkv357.

SPARKS-X – Structure Prediction from Sequence

SPARKS-X

:: DESCRIPTION

SPARKS-X is an improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates.

::DEVELOPER

Sparks Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPARKS-X

:: MORE INFORMATION

Citation

Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou.
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of the query and corresponding native properties of templates.
Bioinformatics 27:2076-82(2011)

MemBrain 20200114 – Transmembrane Protein Structure Prediction

MemBrain 20200114

:: DESCRIPTION

MemBrain is a web server developed for transmembrane protein structure prediction. It contains two main prediction functions, i.e., transmembrane helix (TMH) prediction and TMH-TMH residue contact prediction.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

MemBrain: improving the accuracy of predicting transmembrane helices.
Shen H, Chou JJ.
PLoS One. 2008 Jun 11;3(6):e2399. doi: 10.1371/journal.pone.0002399.

MEMSAT-SVM 1.3 – SVM Transmembrane Protein Structure Prediction

MEMSATSVM 1.3

:: DESCRIPTION

MEMSATSVM is a SVM (support vector machines) based TM (Transmembrane Protein) protein topology predictor.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MEMSAT-SVM

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Jul 17;13:169. doi: 10.1186/1471-2105-13-169.
Detecting pore-lining regions in transmembrane protein sequences.
Nugent T1, Jones DT.

Timothy Nugent and David T Jones
Transmembrane protein topology prediction using support vector machines
BMC Bioinformatics 2009, 10:159

TRFolder / TRFolder-W – Telomerase RNA Structure Prediction

TRFolder /  TRFolder-W

:: DESCRIPTION

TRFolder is a utility program capable of searching for the core structure (including pseudoknots and triple helices) of telomerase RNAs. It consists of a set of functions for telomerase RNA (TR) specific structure prediction. Unlike existing general purpose structure prediction programs, TRFolder works progressively to predict core TR elements pseudoknots, triple helices, telomere repeat template boundary elements, and core-closing stems that occur in TRs.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier
  • Python

:: DOWNLOAD

 TRFolder

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 15;28(20):2696-7. doi: 10.1093/bioinformatics/bts506. Epub 2012 Aug 24.
TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.
Zhang D1, Xue X, Malmberg RL, Cai L.

Guo, L., Zhang, D., Wang, Y., Malmberg, R., McEachern, M., and Cai, L. (2011)
TRFolder: Computational prediction of novel telomerase RNAs in yeast genomes
Int J Bioinform Res Appl. 2011;7(1):63-81.

MEMSAT 3 – Transmembrane Protein Structure Prediction

MEMSAT 3

:: DESCRIPTION

MEMSAT (MEMbrane protein Structure And Topology) is a program which predicts the secondary structure and topology of all-helix integral membrane proteins based on the recognition of topological models. The original MEMSAT method employed a set of statistical tables (log likelihood ratios) compiled from well- characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. These statistical tables showed definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MEMSAT

:: MORE INFORMATION

Citation

Jones D.T. (2007)
Improving the accuracy of transmembrane protein topology prediction using evolutionary information.
Bioinformatics. 2007 Mar 1;23(5):538-44. Epub 2007 Jan 19.