AIS – Classify Amino Acids

AIS

:: DESCRIPTION

AIS (Almost Invariant Sets) is a program which uses a novel criterion and method to classify amino acids. The goal is to identify sets of amino acids with a high probability of change between elements of the set but small probability of change between different sets by using amino acid replacement matrices and their eigenvectors. After identification of the subsets the quality of the partition is assessed with a conductance measure

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AIS

:: MORE INFORMATION

Citation:

Kosiol et al. (2004),
A new criterion and method for amino acid classification
Journal of Theoretical Biology 228:97-106.

RNAcode 0.3 – Analysis of Protein Coding Potential in Multiple Sequence Alignments

RNAcode 0.3

:: DESCRIPTION

RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAcode

:: MORE INFORMATION

Citation:

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011;17(4):578-94.

PIPs 1.1 – Human Protein-Protein Interaction Predictions

PIPs 1.1

:: DESCRIPTION

PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a na?ve Bayesian classifier to calculate a Score of interaction.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

 NO

:: MORE INFORMATION

Citation

PIPs: human protein–protein interaction prediction database
Mark D. McDowall, Michelle S. Scott and Geoffrey J. Barton
Nucl. Acids Res. (2009) 37 (suppl 1): D651-D656. doi: 10.1093/nar/gkn870

14-3-3-Pred – Webserver to predict 14-3-3-binding sites in Proteins

14-3-3-Pred

:: DESCRIPTION

14-3-3-Pred is a webserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides.
Madeira F, Tinti M, Murugesan G, Berrett E, Stafford M, Toth R, Cole C, MacKintosh C, Barton GJ.
Bioinformatics. 2015 Mar 3. pii: btv133.

SCANPS 2.3.11 – Protein Sequence Scanning Package

SCANPS 2.3.11

:: DESCRIPTION

SCANPS is a sequence database searching program that implements a range of sensitive algorithms for searching protein sequence databases.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SCANPS

:: MORE INFORMATION

Citation:

Thomas P. Walsh1, Caleb Webber, Stephen Searle, Shane S. Sturrock and Geoffrey J. Barton
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
Nucl. Acids Res. (2008) 36 (suppl 2): W25-W29.

Interpol 1.3.1 – Numerical Encoding and Interpolation of Amino Acid Sequences

Interpol 1.3.1

:: DESCRIPTION

The software “Interpol” encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms.

::DEVELOPER

Heider Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 Interpol

:: MORE INFORMATION

Citation

BioData Min. 2011 Jun 17;4:16. doi: 10.1186/1756-0381-4-16.
Interpol: An R package for preprocessing of protein sequences.
Heider D1, Hoffmann D.

EFIN – Evaluation of Functional Impact of Nonsynonymous SNPs

EFIN

:: DESCRIPTION

EFIN is a free tool which predict whether amino acids substitution would related to disease evaluated by random forests based on protein conservation.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jun 10;15:455. doi: 10.1186/1471-2164-15-455.
EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome.
Zeng S, Yang J, Chung BH, Lau YL, Yang W

PrOCoil 2.14.0 – Predicting the Oligomerization of Coiled Coil Proteins

PrOCoil 2.14.0

:: DESCRIPTION

The PrOCoil package allows to predict whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  PrOCoil

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2011 May;10(5):M110.004994. doi: 10.1074/mcp.M110.004994. Epub 2011 Feb 10.
Complex networks govern coiled-coil oligomerization–predicting and profiling by means of a machine learning approach.
Mahrenholz CC1, Abfalter IG, Bodenhofer U, Volkmer R, Hochreiter S.

SMART 8.0 – Analysis of Protein Domain Architectures

SMART 8.0

:: DESCRIPTION

SMART (Simple Modular Architecture Research Tool) is an online resource for the identification and annotation of protein domains and the analysis of protein domain architectures.More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Letunic I, Doerks T, Bork P
SMART: recent updates, new developments and status in 2015
Nucleic Acids Res 2014; doi:10.1093/nar/gku949

Letunic et al. (2012)
SMART 7: recent updates to the protein domain annotation resource
Nucleic Acids Res , doi:10.1093/nar/gkr931

AnDom – Assign Structual Domains to Protein Sequences

AnDom

:: DESCRIPTION

AnDom (Annotation of Domains)is a WEB tool helps to assign structual domains to protein sequences and to classify them according to SCOP.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Chem Inf Comput Sci. 2002 Mar-Apr;42(2):405-7.
A versatile structural domain analysis server using profile weight matrices.
Schmidt S, Bork P, Dandekar T.