Tag: TARGETING

TPpred 3.0 – Detection of Mitochondrial-targeting Signals in Proteins

TPpred 3.0

:: DESCRIPTION

TPpred is a web server for MITOCHONDRIAL targeting peptides prediction in proteins. TPpred is optimized for the prediction of cleavage sites of mitochondrial targeting peptides.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BioPython
  • EMBOSS

:: DOWNLOAD

  TPpred

:: MORE INFORMATION

Citation

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in Eukaryotic proteins.
Savojardo C, Martelli PL, Fariselli P, Casadio R.
Bioinformatics. 2015 Jun 16. pii: btv367

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
Savojardo C, Martelli PL, Fariselli P, Casadio R.
Bioinformatics. 2014 Jun 27. pii: btu411.

TargetSOS – Supervised Over-sampling Predictor for Targeting Protein-nucleotide Binding Residues

TargetSOS

:: DESCRIPTION

TargetSOS is a predictor based on the proposed over-sampling algorithm which implemented for protein-nucleotide binding residue prediction.

::DEVELOPER

Pattern Recognition and Bioinformatics Group (Shen Group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

A new supervised over-sampling algorithm with application to protein-nucleotide binding residue prediction.
Hu J, He X, Yu DJ, Yang XB, Yang JY, Shen HB.
PLoS One. 2014 Sep 17;9(9):e107676. doi: 10.1371/journal.pone.0107676.

TargetS – Predictor for Targeting Protein-ligand Binding Sites

TargetS

:: DESCRIPTION

TargetS is a new ligand-specific template-free predictor for targeting protein-ligand binding sites from primary sequences.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):994-1008. doi: 10.1109/TCBB.2013.104.
Designing template-free predictor for targeting protein-ligand binding sites with classifier ensemble and spatial clustering.
Dong-Jun Yu, Jun Hu, Jing Yang, Hong-Bin Shen, Jinhui Tang, and Jing-Yu Yang,

TargetVita – Vitamin-specific Predictor for Targeting Protein-vitamin Binding Residues

TargetVita

:: DESCRIPTION

TargetVita is a new predictor which designed and implemented for predicting protein-vitamin binding residues using protein sequences.

::DEVELOPER

Pattern Recognition and Bioinformatics Group (Shen Group)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Sep 5;15:297. doi: 10.1186/1471-2105-15-297.
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.
Yu DJ1, Hu J, Yan H, Yang XB, Yang JY, Shen HB.

TARGETING 1.0 – Solver for the Maximal Pairing Problem on Arbitrary Trees

TARGETING 1.0

:: DESCRIPTION

TARGETING  is an efficient solver for the Maximal Pairing Problem on arbitrary trees.The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TARGETING

:: MORE INFORMATION

Citation

Arnold, C. and Stadler, PF. 2010.
Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees.
Algorithms for Molecular Biology.