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.

PS-HomPPI v1.3 / NPS-HomPPI – Protein-Protein Binding Site Predictor

PS-HomPPI v1.3 / NPS-HomPPI

:: DESCRIPTION

PS-HomPPI is a sequence-based partner-specific protein-protein interface residue prediction server.

NPS-HomPPI is a sequence-based non-partner-specific protein-protein interface residue prediction server.

::DEVELOPER

Artificial Intelligence Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Jun 17;12:244. doi: 10.1186/1471-2105-12-244.
HomPPI: a class of sequence homology based protein-protein interface prediction methods.
Xue LC1, Dobbs D, Honavar V.

PLEK 1.2 – Predictor of Long Non-coding RNAs and mRNAs based on K-mer Scheme

PLEK 1.2

:: DESCRIPTION

PLEK uses an improved computational pipeline based on k-mer and support vector machine (SVM) to distinguish long non-coding RNAs (lncRNAs) from messager RNAs (mRNAs).

::DEVELOPER

PLEK team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C/C++ compiler
  • Python

:: DOWNLOAD

 PLEK

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Sep 19;15:311. doi: 10.1186/1471-2105-15-311.
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.
Li A, Zhang J1, Zhou Z..

DomEx – Extending Protein Domain Boundary Predictors

DomEx

:: DESCRIPTION

DomEx is an Extending Protein domain predictors to detect discontinuous domains

::DEVELOPER

zhidong xue (zdxue@hust.edu.cn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 DomEx

:: MORE INFORMATION

Citation

Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains.
Xue Z, Jang R, Govindarajoo B, Huang Y, Wang Y.
PLoS One. 2015 Oct 26;10(10):e0141541. doi: 10.1371/journal.pone.0141541.

DisPredict 1.0 – Disorder Protein Predictor

DisPredict 1.0

:: DESCRIPTION

DisPredict is a software for predicting disorder protein.

::DEVELOPER

Hoque’s Lab, University of New Orleans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DisPredict

:: MORE INFORMATION

Citation

DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel.
Iqbal S, Hoque MT.
PLoS One. 2015 Oct 30;10(10):e0141551. doi: 10.1371/journal.pone.0141551.

ProQ2 / ProQM – Membrane Protein / Protein Quality Predictor

ProQ2 / ProQM

:: DESCRIPTION

ProQ2 (Protein Quality Predictor) is a neural network based predictor that based on a number of structural features predicts the quality of a protein model. ProQ is optimized to find correct models in contrast to other methods which are optimized to find native structures.

ProQM method uses a support vector machine with a combination of general and membrane protein-specific features.

::DEVELOPER

‪Björn Wallner‬

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ProQ2 / ProQM

:: MORE INFORMATION

Citation:

ProQ2: Estimation of Model Accuracy Implemented in Rosetta.
Uziela K, Wallner B.
Bioinformatics. 2016 Jan 5. pii: btv767.

Improved model quality assessment using ProQ2.
Arjun Ray, Erik Lindahl and B. Wallner.
BMC Bioinformatics 2012, 13:224, doi:10.1186/1471-2105-13-224

Bioinformatics. 2010 Dec 15;26(24):3067-74. doi: 10.1093/bioinformatics/btq581. Epub 2010 Oct 14.
Model quality assessment for membrane proteins.
Ray A, Lindahl E, Wallner B.

BETApro 1.0 – Protein Beta Sheet Predictor

BETApro 1.0

:: DESCRIPTION

BETApro is a software of prediction of beta-residue pairs, beta-strand pairs, strand alignment, pairing direction, and beta-sheet topology.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BETApro

:: MORE INFORMATION

Citation:

Jianlin Cheng and Pierre Baldi,
Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms,
Bioinformatics, vol. 21(Suppl 1), pp. i75-84, 2005.

MDCAP – MiRNA-Disease Causal Association Predictor

MDCAP

:: DESCRIPTION

The MDCAP is a computinal model for predicting novel causal miRNA-disease associations. MDCAP would calculate a score for all potential causal miRNA-disease associations. With the score, users could identify most potential causal miRNAs for a given disease or new causal associated disease of a miRNA.

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

MDCAP

:: MORE INFORMATION

Citation

Gao Y, Jia K, Shi J, Zhou Y, Cui Q.
A Computational Model to Predict the Causal miRNAs for Diseases.
Front Genet. 2019 Oct 3;10:935. doi: 10.3389/fgene.2019.00935. PMID: 31632446; PMCID: PMC6786093.

PAIRPred 1.0 – Partner Aware Interacting Residue PREDictor

PAIRPred 1.0

:: DESCRIPTION

PAIRPred is a partner specific protein-protein interaction site predictor that can make accurate predictions of whether a pair of residues from two different proteins interact or not.

::DEVELOPER

PAIRPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PAIRPred

:: MORE INFORMATION

Citation

PAIRpred: partner-specific prediction of interacting residues from sequence and structure.
Minhas Fu, Geiss BJ, Ben-Hur A.
Proteins. 2014 Jul;82(7):1142-55. doi: 10.1002/prot.24479.