IntFOLD 5.0 – Integrated Protein Structure and Function Prediction Server

IntFOLD 5.0

:: DESCRIPTION

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.
McGuffin LJ, Atkins JD, Salehe BR, Shuid AN, Roche DB.
Nucleic Acids Res. 2015 Mar 27. pii: gkv236.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W171-6. doi: 10.1093/nar/gkr184. Epub 2011 Mar 31.
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.
Roche DB1, Buenavista MT, Tetchner SJ, McGuffin LJ.

Buenavista, M. T., Roche, D. B., & McGuffin, L. J. (2012)
Improvement of 3D protein models using multiple templates guided by single-template model quality assessment.
Bioinformatics, 28, 1851-1857

CellPPD-Mod – Modified Cell Penetrating Peptides Prediction Server

CellPPD-Mod

:: DESCRIPTION

CellPPD-Mod is an in silico method, which is developed to predict efficient modified cell penetrating peptides. This webserver has been designed to assist the scientific community to predict the cell penetrating potential of modified cell penetrating peptide having natural and chemically modified amino acid residues.

::DEVELOPER

CellPPD-Mod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Prediction of Cell-Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues.
Kumar V, Agrawal P, Kumar R, Bhalla S, Usmani SS, Varshney GC, Raghava GPS.
Front Microbiol. 2018 Apr 12;9:725. doi: 10.3389/fmicb.2018.00725.

EGPred – Eukaryotic Gene Prediction Server

EGPred

:: DESCRIPTION

 EGPred allows to predict gene (protein coding regions) in eukaryote genomes that includes introns and exons, using similarity aided (double) and consensus Ab Intion methods.

::DEVELOPER

EGPred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Issac, B and Raghava, G P S (2004),
EGPred: Prediction of Eukaryotic Genes Using ab initio Methods After Combining With Sequence Similarity Approaches,
Genome Res 14, 1756-1766.

ABCpred – Artificial Neural Network based B-cell Epitope Prediction Server

ABCpred

:: DESCRIPTION

ABCpred server is to predict linear B cell epitope regions in an antigen sequence, using artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research.

::DEVELOPER

ABCpred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha, S and Raghava G.P.S. (2006)
Prediction of Continuous B-cell Epitopes in an Antigen Using Recurrent Neural Network.
Proteins,65(1),40-48

nHLAPred – Neural Network based MHC Class-I Binding Peptide Prediction Server

nHLAPred

:: DESCRIPTION

nHLAPred allow to predict binding peptide for 67 MHC Class I alleles. This also allow to predict the proteasome cleavage site and binding peptide that have cleavage site at C terminus (potential T cell epitopes).

::DEVELOPER

nHLAPred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bhasin M. and Raghava G P S (2006)
A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes;
J. Biosci. 32:31-42.

VGIchan – Voltage Gated Ion Channel Prediction server

VGIchan

:: DESCRIPTION

The aim of VGIchan is to predict voltage gated ion-channels and classify them into sodium, potassium, calcium and chloride ion channels from primary amino sequences.

::DEVELOPER

VGIchan Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha, S., Zack, J., Singh, B. and Raghava, G. P. S. (2007)
VGIchan: Prediction and classification of voltage-gated ion channels.
Genomics Proteomics Bioinformatics. 2006 Nov;4(4):253-8.

PSOPIA 20130501 – Prediction Server of Protein-Protein Interactions

PSOPIA 20130501

:: DESCRIPTION

PSOPIA (Prediction Server Of Protein-protein InterActions) is an AODE for predicting protein-protein interactions using three seqeucne based features; (I) sequence similarities to a known interacting protein pair, (II) statistical propensities of domain pairs observed in interacting proteins and (III) a sum of edge weights along the shortest path between homologous proteins in a PPI network.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 23;15:213. doi: 10.1186/1471-2105-15-213.
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.
Murakami Y, Mizuguchi K.

PCI-SUMO – PCI-Based Sumo Site Prediction Server

PCI-SUMO

:: DESCRIPTION

PCI-SUMO is a method of predicting post-translational sumoylation sites on proteins via parallel cascade identification.

::DEVELOPER

Green lab at Carleton University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Green, J.R., Dmochowski G.M., Golshani A.,
“Prediction of Protein Sumoylation Sites Via Parallel Cascade Identification”,
CMBEC06, Vancouver, 1-3 June 2006.

PCI-SS – PCI-Based Protein Scondary Structure Site Prediction Server

PCI-SS

:: DESCRIPTION

PCI-SS is a method of predicting protein secondary structure using a PCI-based classifier and also a consensus method to combine PCI with PSIPRED.

::DEVELOPER

Green lab at Carleton University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Green, J.R., Korenberg, M.J., and Aboul-Magd, Md., 2009,
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
BMC Bioinformatics 2009, 10:222 doi:10.1186/1471-2105-10-222

SVM-PB-Pred – Protein Block (PB) prediction server

SVM-PB-Pred

:: DESCRIPTION

The SVM-PB-Pred is a Protein Block (PB) prediction server based on Support Vector Machine (SVM) approach.

::DEVELOPER

Research Group of Dr.S.Parthasarathy

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Protein Pept Lett. 2014;21(8):736-42.
SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures.
Suresh V, Parthasarathy S