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.

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.

KnotShape / KnotStructure – Shape and Structure Prediction for ncRNAs including Pseudoknots

KnotShape / KnotStructure

:: DESCRIPTION

KnotShape / KnotStructure was applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots.

::DEVELOPER

KnotShape / KnotStructure team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KnotShape / KnotStructure

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 2:S1. doi: 10.1186/1471-2105-14-S2-S1. Epub 2013 Jan 21.
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.
Achawanantakun R1, Sun Y.

1D – Protein Structure Prediction Server

1D

:: DESCRIPTION

1D server (integrated server for prediction of fold, structural class and secondary structure content).

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Java JRE

:: DOWNLOAD

 1D

:: MORE INFORMATION

Citation

Fold Type Prediction
Chen K, Kurgan LA, 2007.
PFRES: Protein Fold Classification by Using Evolutionary Information and Predicted Secondary Structure.
Bioinformatics, 23(21):2843-2850.

Structural Class Prediction
Chen K, Kurgan LA, Ruan J, 2008.
Prediction of Protein Structural Class Using Novel Evolutionary Collocation Based Sequence Representation.
Journal of Computational Chemistry, 29(10):1596-1604.

Secondary Structure Content Prediction
Homaeian L, Kurgan LA, Cios KJ, Ruan J, Chen K, 2007.
Prediction of Protein Secondary Structure Content for the Twilight Zone Sequences.
Proteins: Structure, Function, and Bioinformatics, 69(3):486-498.

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

Laboratory of Structural Bioinformatics and Design

:: 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)

SPACE – Tools for Structure Prediction and Analysis based on Complementarity with Environment

SPACE

:: DESCRIPTION

SPACE is a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes.

::DEVELOPER

Edelman-Sobolev Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPACE

:: MORE INFORMATION

Citation:

SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment.
Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W39-43.

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.

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.