ANOLEA 2.4.2-2 – Assess the Quality of a 3D Protein Structure

ANOLEA 2.4.2-2

:: DESCRIPTION

ANOLEA (Atomic Non-Local Environment Assessment) is a server to assess the quality of a three – dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ANOLEA

:: MORE INFORMATION

Citation

Proc Int Conf Intell Syst Mol Biol. 1997;5:187-90.
ANOLEA: a www server to assess protein structures.
Melo F, Devos D, Depiereux E, Feytmans E.

Binnacle – Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins

Binnacle

:: DESCRIPTION

binnacle is a tool for binning metagenomic datasets using assembly graphs and scaffolds generated by metacarvel.

::DEVELOPER

MarBL (Maryland Bioinformatics Labs)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

binnacle

:: MORE INFORMATION

Citation

Muralidharan HS, Shah N, Meisel JS, Pop M.
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.
Front Microbiol. 2021 Feb 24;12:638561. doi: 10.3389/fmicb.2021.638561. PMID: 33717033; PMCID: PMC7945042.

BIGpre 2.0.2 – Quality Assessment software for both Illumina and 454 platforms

BIGpre 2.0.2

:: DESCRIPTION

BIGpre is a quality assessment package for next-genomics sequencing data

::DEVELOPER

BIGpre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIGpre

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44. doi: 10.1016/S1672-0229(11)60027-2.
BIGpre: a quality assessment package for next-generation sequencing data.
Zhang T1, Luo Y, Liu K, Pan L, Zhang B, Yu J, Hu S.

ProQ2 / ProQM – Membrane Protein / Protein Quality Predictor

ProQ2 / ProQM

:: DESCRIPTION

ProQ2 (Protein Quality Predictor) is a neural network based predictor that based on a number of structural features predicts the quality of a protein model. ProQ is optimized to find correct models in contrast to other methods which are optimized to find native structures.

ProQM method uses a support vector machine with a combination of general and membrane protein-specific features.

::DEVELOPER

‪Björn Wallner‬

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ProQ2 / ProQM

:: MORE INFORMATION

Citation:

ProQ2: Estimation of Model Accuracy Implemented in Rosetta.
Uziela K, Wallner B.
Bioinformatics. 2016 Jan 5. pii: btv767.

Improved model quality assessment using ProQ2.
Arjun Ray, Erik Lindahl and B. Wallner.
BMC Bioinformatics 2012, 13:224, doi:10.1186/1471-2105-13-224

Bioinformatics. 2010 Dec 15;26(24):3067-74. doi: 10.1093/bioinformatics/btq581. Epub 2010 Oct 14.
Model quality assessment for membrane proteins.
Ray A, Lindahl E, Wallner B.

InfoTrim – DNA Read Quality Trimmer using Entropy Created with Python

InfoTrim

:: DESCRIPTION

InfoTrim is a DNA read quality trimmer based on the Trimmomatic maximum information criterion model.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

InfoTrim

:: MORE INFORMATION

Citation

InfoTrim: A DNA read quality trimmer using entropy
2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

CuReSim 1.3 / CuReSimEval 1.1 – Customized Read Simulator / Evaluate Mapping Quality of CuReSim Simulated Reads

CuReSim 1.3 / CuReSimEval 1.1

:: DESCRIPTION

CuReSim is a customized tool which generates synthetic New-Generation Sequencing reads, supporting read simulation for major letter-base sequencing platforms.

CuReSimEval is a tool to evaluate the mapping quality of the CuReSim simulated reads.

::DEVELOPER

CuReSim team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

 CuReSim , CuReSimEval

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.
Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.
Caboche S1, Audebert C, Lemoine Y, Hot D.

Coval 1.5 – Improving the Quality of Short Read Alignment data

Coval 1.5

:: DESCRIPTION

Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification.

::DEVELOPER

Coval team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 Coval 

:: MORE INFORMATION

Citation

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R.
PLoS One. 2013 Oct 8;8(10):e75402. doi: 10.1371/journal.pone.0075402

ModFOLD 6 – Model Quality Assessment Server

ModFOLD 6

:: DESCRIPTION

The ModFOLD server is the latest version of server for the estimation of both the global and local (per-residue) quality of 3D protein models.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ModFOLD

:: MORE INFORMATION

Citation

Maghrabi, A.H.A. & McGuffin, L.J. (2017)
ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins,
Nucleic Acids Res. 2017 Jul 3;45(W1):W416-W421. doi: 10.1093/nar/gkx332.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W368-72. doi: 10.1093/nar/gkt294. Epub 2013 Apr 25.
The ModFOLD4 server for the quality assessment of 3D protein models.
McGuffin LJ1, Buenavista MT, Roche DB.

FRST 1.2 – Protein Model Quality Estimation Method

FRST 1.2

:: DESCRIPTION

FRST serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure. The energy profile can be visualized in different ways, including a per-residue plot and a colored structure representation, accessible as a series of dynamic web pages.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FRST

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto.
The Victor/FRST Function for Model Quality Estimation.
Journal of Computational Biology 2005; 12(10):1316-1327

ChiLin 2.1 – ChIP-seq Data quality and Analysis Pipeline

ChiLin 2.1

:: DESCRIPTION

ChiLin provides a more flexible handle for understanding the ChIP-seq analysis workflow.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ChiLin

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Oct 3;17(1):404.
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
Qin Q, et al.

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