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.

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

Stockholm Bioinformatics Center

:: 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.

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

zqFold – Predicting RNA Secondary Structure

zqFold

:: DESCRIPTION

zqFold is a simple software for predicting RNA secondary structure. The most development from RNAstructure is that it can predict based on species. For example, if you choose ‘tRNA’, and the sequence will be folded as a cloverleaf; if you choose ‘siRNA’ or ‘microRNA precursor’, it will be folded as a hairpin.

::DEVELOPER

Dr. Quan Zou , Tuo Zhao ,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 zqFold

:: MORE INFORMATION

Citation

Quan Zou, Tuo Zhao, Yang Liu, Maozu Guo.
Predicting RNA secondary structure based on the class information and Hopfield network.
Computers in Biology and Medicine. 2009,39(3):206-214

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.

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.

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.

SubChlo 2.0 – Predicting Protein Subchloroplast Locations

SubChlo 2.0

:: DESCRIPTION

SubChlo is the first computational system for predicting protein subchloroplast locations from its primary sequence.

::DEVELOPER

Bioinformatics Division / Center for Synthetic and Systems Biology, TNLIST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Perl / .net 2.0

:: DOWNLOAD

 SubChlo

:: MORE INFORMATION

Citation

J Theor Biol. 2009 Nov 21;261(2):330-5. doi: 10.1016/j.jtbi.2009.08.004. Epub 2009 Aug 11.
SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm.
Du P, Cao S, Li Y.

McQFold – Predicting RNA Secondary Structures with Pseudoknots by MCMC Sampling

McQFold

:: DESCRIPTION

McQFold is a program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence.

::DEVELOPER

Dirk Metzler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C++ Compiler

:: DOWNLOAD

 McQFold

:: MORE INFORMATION

Citation

J Math Biol. 2008 Jan;56(1-2):161-81. Epub 2007 Jun 23.
Predicting RNA secondary structures with pseudoknots by MCMC sampling.
Metzler D, Nebel ME.

N-Ace – Predicting Protein N-Acetylation site

N-Ace

:: DESCRIPTION

N-Ace is a web tool for predicting the protein Acetylation site based on Support Vector Machine (SVM), which is training depend on the amino acid sequence and other structural characteristics, such as accessible surface area, absolute entropy, non-bonded energy, size, amino acid composition, steric parameter, hydrophobicity, volume, mean polarity, electric charge, heat capacity and isoelectric point which is surrounding the modification site and implemented two stages SVM method.

::DEVELOPER

Integrative System Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Comput Chem. 2010 Nov 30;31(15):2759-71. doi: 10.1002/jcc.21569.
N-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.
Lee TY, Hsu JB, Lin FM, Chang WC, Hsu PC, Huang HD.