FREAD 3.0.1 – Database Search Loop Structure Prediction protocol

FREAD 3.0.1

:: DESCRIPTION

FREAD is a database search loop structure prediction protocol. Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

FREAD

Citation

FREAD revisited: Accurate loop structure prediction using a database search algorithm.
Choi Y, Deane CM.
Proteins. 2010 May 1;78(6):1431-40. doi: 10.1002/prot.22658.

Cycloquest 20110907 – Identification of Cyclopeptides via Database Search

Cycloquest 20110907

:: DESCRIPTION

Cycloquest is a software of identification of cyclopeptides via database search of their mass spectra against genome databases.

::DEVELOPER

Hosein Mohimani

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

  Cycloquest

:: MORE INFORMATION

Citation

Cycloquest: Identification of Cyclopeptides via Database Search of Their Mass Spectra against Genome Databases.
Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner PA.
J Proteome Res. 2011 Sep 7.

MS-GF+ 20140630 – Database search for Peptide Identification

MS-GF+ 20140630

:: DESCRIPTION

MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MS-GF+

:: MORE INFORMATION

Citation

MS-GF+ makes progress towards a universal database search tool for proteomics.
Kim S, Pevzner PA.
Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.

deconSTRUCT – Protein Structure Comparison and Database Search

deconSTRUCT

:: DESCRIPTION

deconSTRUCT is a server for fast searching through PDB (and some of its subsets) using a piece of structure as a query – among other things, the superimposed structures are downloadable as Pymol, Chimera and Yasara sessions.

::DEVELOPER

Evolution of Protein Structure and Function Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W590-4. doi: 10.1093/nar/gkq489. Epub 2010 Jun 3.
deconSTRUCT: general purpose protein database search on the substructure level.
Zhang ZH, Bharatham K, Sherman WA, Mihalek I.

Exalign 1.0 – Gene Structural Alignments and Database Search

Exalign 1.0

:: DESCRIPTION

Exalign is a tool that performs alignments of gene exonic structures. In particular it works by aligning arrays representing the exon lengths of genes. While the aligning algorithms used by Exalign are the well known Smith-Waterman and Needleman-Wunsch ones (with a suitable scoring function), the program performs a post-processing step that tries to identify intron gain/loss events (see sections about exon merging).

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Complier

:: DOWNLOAD

 Exalign

:: MORE INFORMATION

Citation:

Pavesi G, Zambelli F, Caggese C, Pesole G.
Exalign: a new method for comparative analysis of exon-intron gene structures.
Nucleic Acids Res. 2008 May;36(8):e47. Epub 2008 Apr 8.

COPS Benchmark 2009/6 – Interactive Analysis of Database Search Methods

COPS Benchmark 2009/6

:: DESCRIPTION

The COPS benchmark provides a standardized tool for the analysis of sequence alignment methods, homology search tools and fold recognition techniques which is easy to use. Most importantly, any method can be immediately related to several popular methods. Hence, the server is a useful tool for a wide range of problems encountered in bioinformatics, and in particular for algorithm developers and for all users who need to understand the range of applicability of various alignment methods.

::DEVELOPER

C.A.M.E. – the Center of Applied Molecular Engineering.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 COPS Benchmark

:: MORE INFORMATION

Citation

Frank, K., Gruber, M. & Sippl, M.J.
COPS Benchmark: interactive analysis of database search methods.
Bioinformatics Vol. 26(4), pp. 574-575