NeuroPID 201503 – Neuropeptide-Precursor Identifier

NeuroPID 201503

:: DESCRIPTION

NeuroPID is a prediction tool for Neuropeptide Precursors (NPPs) and Neuromodulators

::DEVELOPER

The Sudarsky Center for Computational Biology – The Hebrew University of Jerusalem

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NeuroPID: a classifier of neuropeptide precursors.
Karsenty S, Rappoport N, Ofer D, Zair A, Linial M.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W182-6. doi: 10.1093/nar/gku363.

ProFET 1.0 – Protein Feature Engineering Toolkit

ProFET 1.0

:: DESCRIPTION

ProFET: Protein Feature Engineering Toolkit for Machine Learning

::DEVELOPER

Dan Ofer , Michal Linial

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ProFET

:: MORE INFORMATION

Citation

ProFET: Feature engineering captures high-level protein functions.
Ofer D, Linial M.
Bioinformatics. 2015 Jun 30. pii: btv345.

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.

TargetCrys – Protein Crystallization Predictor

TargetCrys

:: DESCRIPTION

TargetCrys is a web server for protein crystallization prediction by fusing multi-view features with two-layered SVM

::DEVELOPER

Pattern Recognition and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hu J, Han K, Li Y, Yang JY, Shen HB, Yu DJ.
TargetCrys: protein crystallization prediction by fusing multi-view features with two-layered SVM.
Amino Acids. 2016 Nov;48(11):2533-2547. doi: 10.1007/s00726-016-2274-4. Epub 2016 Jun 14. PMID: 27299433.

TargetFreeze – Protein Sequence-based AFP predictor

TargetFreeze

:: DESCRIPTION

TargetFreeze is a supplement method to existing AFPs (Antifreeze proteins) predictors and will have potential applications in AFPs-related biotechnology fields.

::DEVELOPER

Pattern Recognition and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Membr Biol. 2015 Jun 10.
TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition.
He X1, Han K, Hu J, Yan H, Yang JY, Shen HB, Yu DJ.

TargetATP – Predicting Protein-ATP Binding Site

TargetATP

:: DESCRIPTION

TargetATP is a full-featured GUI application for targeting protein-ATP binding residues in protein sequences, consisting of two parts of local client and remote server.

::DEVELOPER

Pattern Recognition and Bioinformatics Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Comput Chem. 2013 Apr 30;34(11):974-85. doi: 10.1002/jcc.23219. Epub 2013 Jan 3.
TargetATPsite: a template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble.
Yu DJ1, Hu J, Huang Y, Shen HB, Qi Y, Tang ZM, Yang JY.

TargetDisulfide – Disulfide Connectivity Prediction with Modelled Protein 3D Structural Information and Random Forest Regression

TargetDisulfide

:: DESCRIPTION

TargetDisulfide: Disulfide Connectivity Prediction with Modelled Protein 3D Structural Information and Random Forest Regression

::DEVELOPER

Pattern Recognition and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yu DJ, Li Y, Hu J, Yang X, Yang JY, Shen HB.
Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression.
IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):611-21. doi: 10.1109/TCBB.2014.2359451. PMID: 26357272.

Sherlocc 1.0 – Detect Statistically Relevant Conserved Rare Codon Clusters

Sherlocc 1.0

:: DESCRIPTION

Sherlocc is a PERL written program able to scan Pfam protein families for conserved regions that have a low codon usage frequency (rare codon clusters). This program represents a novel approach as it is efficient enough to perform large-scale analysis of the proteome via the Pfam protein family database (representing about 70% of the known protein universe).

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

Sherlocc

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1438-45. doi: 10.1093/bioinformatics/bts149. Epub 2012 Mar 30.
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.
Chartier M, Gaudreault F, Najmanovich R.

ORION – Profile-profile Fold Recognition

ORION

:: DESCRIPTION

ORION (Optimized fold RecognitION) is a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ORION

:: MORE INFORMATION

Citation

Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.
Ghouzam Y, Postic G, de Brevern AG, Gelly JC.
Bioinformatics. 2015 Aug 7. pii: btv462.

iPBA – Protein Structures Mining and Superimposition

iPBA

:: DESCRIPTION

iPBA is a tool for protein structures mining and superimposition based on similarity in the local backbone conformation.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iPBA: a tool for protein structure comparison using sequence alignment strategies.
Gelly JC, Joseph AP, Srinivasan N, de Brevern AG.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W18-23. doi: 10.1093/nar/gkr333.