FunFOLD 3.0 – Protein-Ligand Binding Site Prediction Server

FunFOLD 3.0

:: DESCRIPTION

The FunFOLD software is freely available as both a standalone package and a prediction server, providing competitive ligand binding site residue predictions for expert and non-expert users alike. The software provides a new fully automated approach for structure based function prediction using 3D models of proteins.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 FunFOLD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 16;12:160. doi: 10.1186/1471-2105-12-160.
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins.
Roche DB1, Tetchner SJ, McGuffin LJ.

PFP / ESG – Sequence Similarity-based Protein Function Prediction server

PFP / ESG

:: DESCRIPTION

PFP (Protein Function Prediction) is a sequence similarity-based protein function prediction server designed to predict GO annotations for a query sequence beyond what can be found by conventional database search such as BLAST.It takes into account weakly similar sequences as well as GO term associations observed in known annotations.

ESG (Extended Similarity Group) is a sequence similarity-based protein function prediction server. It employ PSI-BLAST iteratively and essentially selects GO term annotations that appear consistently in the searches.

Combined PFP & ESG interface.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PFP/ESG: Automated protein function prediction servers enhanced with Gene Ontology visualization tool.
Khan IK, Wei Q, Chitale M, Kihara D.
Bioinformatics. 2015 Jan 15;31(2):271-2. doi: 10.1093/bioinformatics/btu646.

iLoops – Protein-protein Interaction prediction server based on Structural Features

iLoops

:: DESCRIPTION

The iLoops Server uses the loop classification as defined in ArchDB and/or the SCOP classification of domains to predict whether or not a pair of proteins interact.

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2360-2. doi: 10.1093/bioinformatics/btt401. Epub 2013 Jul 9.
iLoops: a protein-protein interaction prediction server based on structural features.
Planas-Iglesias J1, Marin-Lopez MA, Bonet J, Garcia-Garcia J, Oliva B.

CombFunc – Protein Function Prediction Server

CombFunc

:: DESCRIPTION

CombFunc is an automated method for the prediction of protein function. Users can either submit a sequence or use a uniprot identifier.

::DEVELOPER

Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W466-70. doi: 10.1093/nar/gks489. Epub 2012 May 27.
CombFunc: predicting protein function using heterogeneous data sources.
Wass MN, Barton G, Sternberg MJ.

3DLigandSite – Ligand Binding Site Prediction Server

3DLigandSite

:: DESCRIPTION

3DLigandSite is a server that automates a successful manual method for the prediction of protein ligand binding residues in CASP8.

::DEVELOPER

Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W469-73. doi: 10.1093/nar/gkq406. Epub 2010 May 31.
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA, Sternberg MJ.

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.