Tag: Protein Function

Parepro 1.0 – Identify which nsSNP have a deleterious effect on Protein Function

Parepro 1.0

:: DESCRIPTION

Parepro (Prediction of amino acid replacement probability) is a methodof identifying which non-synonymous single base changes have a deleterious effect on protein function, based on support vector machine (SVM).

::DEVELOPER

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows
  • Perl

:: DOWNLOAD

 Parepro

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Nov 16;8:450.
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.
Tian J1, Wu N, Guo X, Guo J, Zhang J, Fan Y.

SIFT 6.2.1 – Amino Acid Substitution Affects Protein Function

SIFT 6.2.1

:: DESCRIPTION

SIFT (Sorting Intolerant From Tolerant) is a program for predicting whether an amino acid substitution affects protein function, based on sequence homology and the physical properties of amino acids. It is one of several programs using sequence information for this purpose.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SIFT

:: MORE INFORMATION

Citation:

Ng PC, Henikoff S. 2002.
Accounting for human polymorphisms predicted to affect protein function.
Genome Research 12:436-446. doi:10.1101/gr.212802

ProMK – Predicting Protein Function using Multiple Kernels

ProMK

:: DESCRIPTION

ProMK is a method of Predicting Protein Function using Multiple Kernels

::DEVELOPER

IDEA Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 ProMK

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):219-33. doi: 10.1109/TCBB.2014.2351821.
Predicting Protein Function Using Multiple Kernels.
Yu G, Rangwala H, Domeniconi C, Zhang G, Zhang Z.

COFACTOR – Structure-based Protein Function Annotation

COFACTOR

:: DESCRIPTION

COFACTOR is a structure-based method for biological function annotation of protein molecules.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W471-7. doi: 10.1093/nar/gks372. Epub 2012 May 8.
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.
Roy A1, Yang J, Zhang Y.

ProteinFuncPred – Protein function prediction

ProteinFuncPred

:: DESCRIPTION

ProteinFuncPred is a sofware of two domain-based protein function prediction methods that encode domain recurrence and order information.

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ProteinFuncPred

:: MORE INFORMATION

Citation

Mario Messih, Meghana Chitale, Vladimir Bajic, Daisuke Kihara, and Xin Gao.
Protein function prediction that considers domain recurrence and order.
Bioinformatics (2012), 28(18): i444–i450. Earlier version appeared in the 11th European Conference on Computational Biology (ECCB2012).

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.

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.

MANGO – Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)

MANGO

:: DESCRIPTION

MANGO is a server for predicting functional class of a protein. It predict function according to GO categories. The method is developed on protein in UNIPROT database whoes function have been assigned manually according to GO criteria.

::DEVELOPER

Dr. G P S Raghava,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2006)
MANGO: prediction of Genome Ontology (GO) class of a protein from its amino acid and dipeptide composition using nearest neighbor approach.
CASP7: 93

ProFunc – Predicting Protein Function from 3D Structure

ProFunc

:: DESCRIPTION

ProFunc helps identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods to try to provide clues as the the protein’s likely or possible function. Often, where one method fails to provide any functional insight another may be more helpful.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W89-93.

AnaGram – Protein Function Prediction

AnaGram

:: DESCRIPTION

AnaGram (the analogy between the text anagrams) is able to propose a function to protein sequences based on finding correlations between short sequences signals and functional annotations in public databases

::DEVELOPER

Bioinformatics and Information Technologies LaboratoryUniversity of Malaga

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

A. J. Pérez, G. Thode and O. Trelles
AnaGram: protein function assignment
Bioinformatics (2004) 20 (2): 291-292.

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