MemType-2L – Predicting Membrane Protein Types

MemType-2L

:: DESCRIPTION

MemType-2L is a 2-layer predictor for predicting membrane protein types, the first layer will predict whether the query sequence belongs to membrane proteins or not; and the second layer aims to predict exactly the membrane protein types when the output of the first layer is “membrane proteins”.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2007 Aug 24;360(2):339-45. Epub 2007 Jun 15.
MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM.
Chou KC1, Shen HB.

Signal-CF – Predicting Signal Peptides

Signal-CF

:: DESCRIPTION

Signal-CF is an automated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2007 Jun 8;357(3):633-40. Epub 2007 Apr 5.
Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides.
Chou KC1, Shen HB.

InterMap3D – Predicting and Visualizing Co-evolving Protein Residues

InterMap3D

:: DESCRIPTION

InterMap3D predicts interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

InterMap3D: predicting and visualizing co-evolving protein residues.
Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG.
Bioinformatics. 2009 Aug 1;25(15):1963-5. doi: 10.1093/bioinformatics/btp335.

MIfold 2 – Predicting RNA Structure using Mutual Information

MIfold 2

:: DESCRIPTION

MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). Given a sequence alignment MIfold computes and displays the mutual and sequence information of the alignment. MIfold also uses a dynamic programming algorithm to predict the secondary structure with maximal total mutual information.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

MIfold

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • matlab

:: DOWNLOAD

 MIfold

:: MORE INFORMATION

Citation

Freyhult, Eva, Moulton, Vincent and Gardner, Paul, 2005
Predicting RNA structure using mutual information,
Applied Bioinformatics. 4(1):53-9.

PhyloRNAalifold v1 – Predicting Consensus Structures in RNA Alignments by incorporating RNAalifold with Phylogenetic information

PhyloRNAalifold v1

:: DESCRIPTION

PhyloRNAalifold is a program for predicting consensus structures of aligned RNA sequences by incorporating phylogetetic-based covarying mutations.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PhyloRNAalifold

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Apr 27;14:142. doi: 10.1186/1471-2105-14-142.
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.
Ge P, Zhang S.

RNAConSLOpt 1.2 – Predicting Consensus stable local optimal Structures for Aligned RNA Sequences

RNAConSLOpt 1.2

:: DESCRIPTION

RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAConSLOpt

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):498-518. doi: 10.1504/IJBRA.2014.062997.
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Li Y, Zhong C, Zhang S.

RNASLOpt – Predicting stable local optimal Structures for RNAs

RNASLOpt

:: DESCRIPTION

RNASLOpt is a program for predicting stable local optimal secondary structures (represented by stack configurations) for RNAs. RNASLOpt can be used to predict alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNASLOpt

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Nov 1;27(21):2994-3001. doi: 10.1093/bioinformatics/btr510. Epub 2011 Sep 8.
Finding stable local optimal RNA secondary structures.
Li Y, Zhang S.

RNAEAPath 1.0 – Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks

RNAEAPath 1.0

:: DESCRIPTION

RNAEAPath provides an alternate approach for predicting low-barrier folding pathways between RNA conformational secondary structures.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAEAPath

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S5. doi: 10.1186/1471-2105-13-S3-S5.
Predicting folding pathways between RNA conformational structures guided by RNA stacks.
Li Y, Zhang S.

ProMK – Predicting Protein Function using Multiple Kernels

ProMK

:: DESCRIPTION

ProMK is a method of Predicting Protein Function using Multiple Kernels

::DEVELOPER

Guoxian Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 ProMK

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):219-33. doi: 10.1109/TCBB.2014.2351821.
Predicting Protein Function Using Multiple Kernels.
Yu G, Rangwala H, Domeniconi C, Zhang G, Zhang Z.

BinMemPredict – Predicting Membrane Protein Types

BinMemPredict

:: DESCRIPTION

BinMemPredict is a platform that supports users to submit multiple sequences for prediction at one time. It offers two kinds of features to train model, one of which is 20-D feature based on PSSM matrix and the other is 188-D feature based on the composition and physical-chemical properties.

::DEVELOPER

Data Mining Group, Xiamen University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA

:: DOWNLOAD

 BinMemPredict

:: MORE INFORMATION

Citation

Quan Zou, Xubin Li, Yi Jiang, Yuming Zhao, Guohua Wang.
BinMemPredict: a Web server and software for predicting membrane protein types.
Current Proteomics. 2013, 10(1): 2-9