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

NTXpred – Prediction of Neurotoxins from their Function and Source

NTXpred

:: DESCRIPTION

The aim of NTXpred is to predict neurotoxins and it source and probable functions from primary amino acid sequences

::DEVELOPER

NTXpred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha, S. and Raghava, G. P. S. (2007)
Prediction of neurotoxins based on their function and source.
In Silico Biology 7, 0025

I-TASSER 5.1 – Protein Structure & Function Predictions

I-TASSER 5.1

:: DESCRIPTION

I-TASSER was ranked best in tertiary structure prediction (as ‘Zhang-Server’) in the community-wide blind benchmarks CASP7 and CASP8. It uses mainly profile-profile comparison to identify templates and alignments for deriving distance constraints. Its power lies in how it combines the distance constraints from up to the 50 best-ranked templates. It performs some knowledge-based free modelling in regions without any template-based information.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 I-TASSER

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 16. pii: gkv342.
I-TASSER server: new development for protein structure and function predictions.
Yang J, Zhang Y

Ambrish Roy, Alper Kucukural, Yang Zhang.
I-TASSER: a unified platform for automated protein structure and function prediction.
Nature Protocols, vol 5, 725-738 (2010)

NRProF – Protein Function Prediction Based on the Neural Response Algorithm

NRProF

:: DESCRIPTION

 NRProF is a novel automated protein functional assignment method based on the neural response algorithm, which simulates the neuronal behavior of the visual cortex in the human brain. The main idea of this algorithm is to define a distance metric that corresponds to the similarity of the subsequences and reflects how the human brain can distinguish between different sequences. We predicted the most similar target protein for a given query protein using the two layered neural response algorithm and thereby assigned the GO term associated with the target sequence to the query sequence. Our method predicted and ranked the actual GO term in the first position out of five with an accuracy of 82%. Results of the 5-fold cross validation and the comparison with PFP server indicate the better performance by our method.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package

:: DOWNLOAD

 NRProF

:: MORE INFORMATION

Citation

Hari Krishna Yalamanchili, Quan-Wu Xiao, and Junwen Wang .
A novel neural response algorithm for protein function prediction
BMC Systems Biology 2012, 6(Suppl 1):S19

DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.

MuD – Annotating the Affect of Missense Mutations on the Protein’s Function

MuD

:: DESCRIPTION

MuD (Mutation Detector) is a server for annotating the affect of missense mutations on the protein’s function using sequence and structural features

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W523-8. doi: 10.1093/nar/gkq528. Epub 2010 Jun 11.
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N.

DNAlive – Display DNA Structural Features in relation with Genome Annotations and Functions

DNAlive

:: DESCRIPTION

 DNAlive displays DNA structure features in relation with genome annotations and functions.DNAlive is a tool for the analysis of structural and physical characteristics of genomic DNA.

::DEVELOPER

Molecular Modelling & Bioinformatics Unit. IRB Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1731-2. Epub 2008 Jun 9.
DNAlive: a tool for the physical analysis of DNA at the genomic scale.
Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M.

spkTools 1.27.0 – Collection of Functions to Analyze Microarray Spike-in data

spkTools 1.27.0

:: DESCRIPTION

spkTools contains functions that can be used to compare expression measures on different array platforms.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 spkTools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Oct;36(17):e108. doi: 10.1093/nar/gkn430. Epub 2008 Aug 1.
Consolidated strategy for the analysis of microarray spike-in data.
McCall MN, Irizarry RA.

SpectralTDF – Spectral Representation of Transition Density Functions

SpectralTDF

:: DESCRIPTION

SpectralTDF is a program for computing the transition density function (TDF) of the diffusion approximation of the Wright-Fisher process with general diploid selection and recurrent mutation.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX / WIndows
  • Java

:: DOWNLOAD

 SpectralTDF

:: MORE INFORMATION

Citation

SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes.
Steinrücken M, Jewett EM, Song YS.
Bioinformatics. 2015 Nov 9. pii: btv627.