Tag: Consensus

conSSert – Consensus Secondary Structure Prediction

conSSert

:: DESCRIPTION

conSSert is a SVM-based consenus secondary structure prediction method. Predictions from four popular secondary structure models (PSSpred, PSIPRED, Raptor-X, and SPINE-X) are integrated through the use of SVM models to produce highly accurate predictions, especially with regard to Q2-EH.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

conSSert: Consensus SVM model for accurate prediction of ordered secondary structure.
Kieslich CA, Smadbeck J, Khoury GA, Floudas C.
J Chem Inf Model. 2016 Feb 29.

AMYLPRED – A Consensus Method for Amyloid Propensity Prediction

AMYLPRED

:: DESCRIPTION

AMYL-PRED is a consensus prediction method for identifying possible amyloidogenic regions in protein sequences.

::DEVELOPER

The Biophysics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Struct Biol. 2009 Jul 9;9:44. doi: 10.1186/1472-6807-9-44.
Amyloidogenic determinants are usually not buried.
Frousios KK, Iconomidou VA, Karletidi CM, Hamodrakas SJ.

Warpgroup 0.1.0 – Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis

Warpgroup 0.1.0

:: DESCRIPTION

Warpgroup is an R package for processing chromatography-mass spectrometry data.

::DEVELOPER

Patti Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • R

:: DOWNLOAD

 Warpgroup

:: MORE INFORMATION

Citation:

Warpgroup: Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis.
Mahieu NG, Spalding J, Patti GJ.
Bioinformatics. 2015 Sep 30. pii: btv564.

AMS 4.0-1.5 – Consensus Prediction of Post-translational Modifications in Protein Sequences

AMS 4.0-1.5

:: DESCRIPTION

AMS (AutoMotif Service) predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences.

::DEVELOPER

AMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 AMS

:: MORE INFORMATION

Citation

Amino Acids. 2012 Aug;43(2):573-82. doi: 10.1007/s00726-012-1290-2.
AMS 4.0: consensus prediction of post-translational modifications in protein sequences.
Plewczynski D, Basu S, Saha I.

PredictSNP2 – Unified Platform for Prediction of SNP effect in Distinct Genomic Regions

PredictSNP2

:: DESCRIPTION

The PredictSNP is a consensus classifier combining six best performing prediction methods to provide more accurate and robust alternative to the predictions delivered by individual integrated tools.

PredictSNP2 extends the scope of genome analysis to the level of nucleotide substitutionsthat enables to identify disease­-related variants within the whole genome.

::DEVELOPER

Protein Engineering Group, Loschmidt Laboratories

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
Bendl J, Musil M, Štourač J, Zendulka J, Damborský J, Brezovský J.
PLoS Comput Biol. 2016 May 25;12(5):e1004962. doi: 10.1371/journal.pcbi.1004962.

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.
Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, Brezovsky J, Damborsky J.
PLoS Comput Biol. 2014 Jan;10(1):e1003440. doi: 10.1371/journal.pcbi.1003440

disCoP – Disorder Consensus-based Predictor

disCoP

:: DESCRIPTION

disCoP method is designed for in-silico prediction of per-residue protein disorder propensities. It combines four rationally selected input predictors: DISOclust, DISOPRED2, MD, and SPINE-D, using custom-designed features that aggregate their predictions and binomial deviance-based regression model.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2014;32(3):448-64. doi: 10.1080/07391102.2013.775969. Epub 2013 Mar 27.
Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus.
Fan X1, Kurgan L.

ILbind – Consensus-based Inverse Ligand Binding Predictor

ILbind

:: DESCRIPTION

ILbind is a consensus predictor that combines the two complementary inverse ligand binding predictors implemented using FINDSITE and SMAP and Support Vector Machines.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ILbind

:: MORE INFORMATION

Citation

Hu G, Gao J, Wang K, Mizianty MJ, Ruan J, Kurgan L.
Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions.
Bioinformatics. 2014 Aug 28. pii: btu581. [Epub ahead of print]

SSCon – Consensus-based Secondary Structure predictor

SSCon

:: DESCRIPTION

SScon is a first-of-its-kind comprehensive design of a SS consensus predictor which considers 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

  SSCon

 :: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2014;32(1):36-51. doi: 10.1080/07391102.2012.746945. Epub 2013 Jan 9.
Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.
Yan J1, Marcus M, Kurgan L.

RNAConSLOpt 1.2 – Predicting Consensus stable local optimal Structures for Aligned RNA Sequences

RNAConSLOpt 1.2

:: DESCRIPTION

RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAConSLOpt

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):498-518. doi: 10.1504/IJBRA.2014.062997.
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Li Y, Zhong C, Zhang S.

RNAscf 1.1 – Consensus Folding of Unaligned RNA sequences

RNAscf 1.1

:: DESCRIPTION

RNAscf is a program for RNA consensus folding for a set of unaligned RNA sequences.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAscf

:: MORE INFORMATION

Citation

J Comput Biol. 2006 Mar;13(2):283-95.
Consensus folding of unaligned RNA sequences revisited.
Bafna V, Tang H, Zhang S.