Check My Metal – Metal Binding Site Validation Server

Check My Metal

:: DESCRIPTION

CMM (Check My Metal) is a web server for the validation of metal binding sites in macromolecules.

::DEVELOPER

Minor Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

BioNetCAD 1.1 – Design, Simulation and Experimental Validation of Synthetic Biochemical Networks

BioNetCAD 1.1

:: DESCRIPTION

BioNetCAD ,a CellDesigner plug-in, is a computer assisted design tool for synthetic biology.

::DEVELOPER

BioNetCAD team

:: SCREENSHOTS

BioNetCAD

:: REQUIREMENTS

:: DOWNLOAD

 BioNetCAD

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Rialle S1, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F.

MergeMaid 2.56.0 – Merging and Cross-study Validation of Gene Expression data

MergeMaid 2.56.0

:: DESCRIPTION

The functions in MergeMaid are intended for cross-study comparison of gene expression array data.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 MergeMaid

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2004;3:Article29. Epub 2004 Oct 31.
MergeMaid: R tools for merging and cross-study validation of gene expression data.
Cope L1, Zhong X, Garrett E, Parmigiani G.

SATIVA 0.9 – Semi-Automatic Taxonomy Improvement and Validation Algorithm

SATIVA 0.9

:: DESCRIPTION

SATIVA is a pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections.

::DEVELOPER

Alexey Kozlov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 SATIVA

:: MORE INFORMATION

Citation

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.
Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.
Nucleic Acids Res. 2016 May 10. pii: gkw396

Twilight – A tool for Ligand Density Validation

Twilight

:: DESCRIPTION

Twilight is a standalone script for analysis, visualization, and annotation of a pre-filtered set of protein/ligand complexes deposited with the PDB with ligand RSCC values that are below a threshold of 0.6.

::DEVELOPER

Twilight team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 Twilight

:: MORE INFORMATION

Citation:

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):195-200. doi: 10.1107/S1744309112044387.
Visualizing ligand molecules in Twilight electron density.
Weichenberger CX1, Pozharski E, Rupp B.

ValWorkBench 1.0 – Java library for Cluster Validation

ValWorkBench 1.0

:: DESCRIPTION

ValWorkBench consists of a collection of measures for validation of clustering solutions and algorithms. It has external measures, as the Adjusted Rand index, and internal measures as Figure of Merit, Gap Statistics, Within Cluster Sum Square, Consensus Clustering and more.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

ValWorkBench

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Java

:: DOWNLOAD

 ValWorkBench

:: MORE INFORMATION

Citation

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.
Giancarlo R, Scaturro D, Utro F.
Comput Methods Programs Biomed. 2015 Feb;118(2):207-17. doi: 10.1016/j.cmpb.2014.12.004.

ProTSAV 1.0 – Protein Tertiary Structure Analysis and Validation server

ProTSAV 1.0

:: DESCRIPTION

ProTSAV is a meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model.

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ProTSAV

:: MORE INFORMATION

Citation:

ProTSAV: A protein tertiary structure analysis and validation server.
Singh A, Kaushik R, Mishra A, Shanker A, Jayaram B.
Biochim Biophys Acta. 2015 Oct 15. pii: S1570-9639(15)00260-5. doi: 10.1016/j.bbapap.2015.10.004.

Peptizer 1.8.4 – Automating manual Validation of MS/MS Search results

Peptizer 1.8.4

:: DESCRIPTION

The Peptizer platform was created to automate the manual validation process by an expert system. The user can create a rule set via by enabling a set of Agent objects that will each inspect an assumption based on expert knowledge. Subsequent aggregation of multiple Agent inspection the enables separation of peptide identifications by these rules.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  Peptizer

:: MORE INFORMATION

Citation

Helsens et al.
Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results.
Molecular & cellular proteomics : MCP (2008) vol. 7 (12) pp. 2363-72.

TAP 1.1 – Protein Structure Validation

TAP 1.1

:: DESCRIPTION

TAP serves to validate the local torsion angles of a protein structure. The server computes both an overall conformational score of a protein structure and a confidence estimate.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TAP

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto and Roberto Battistutta.
TAP score: torsion angle propensity normalization applied to local protein structure evaluation.
BMC Bioinformatics, accepted for publication. (2007)

Xwalk 0.6 – Predication, Validation & Visualisation of Chemical Cross-Link Data

Xwalk 0.6

:: DESCRIPTION

Xwalk allows the user to validate and predict cross-link data by calculating Solvent Accessible Surface Distances (SASD) between amino acids.

::DEVELOPER

Dr. Abdullah Kahraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java
:: DOWNLOAD

 Xwalk 

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2163-4. doi: 10.1093/bioinformatics/btr348. Epub 2011 Jun 11.
Xwalk: computing and visualizing distances in cross-linking experiments.
Kahraman A1, Malmström L, Aebersold R.