SMURF / SMURFLite – Simplified / Structural Motifs Detection Using Random Fields

SMURFLite

:: DESCRIPTION

SMURF is a webserver for protein structural motifs dection using random fields

SMURFLite (simplified Structural Motifs Using Random Fields)  is a web application for protein remote homology detection, specifically in beta-structural proteins.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

M. Menke, B. Berger and L. Cowen,
Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system
PNAS March 2, 2010 vol. 107 no. 9 4069-4074.

Bioinformatics. 2012 May 1;28(9):1216-22. doi: 10.1093/bioinformatics/bts110.
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.
Daniels NM, Hosur R, Berger B, Cowen LJ.

RNArobo 2.1.0 – RNA Structural Motif Search tool

RNArobo 2.1.0

:: DESCRIPTION

RNArobo is an RNA structural motif search tool. RNArobo can search sequence databases in FASTA format for a motif defined by a descriptor, which can specify primary and secondary structure constraints.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RNArobo

:: MORE INFORMATION

Citation

RNA motif search with data-driven element ordering.
Rampášek L, Jimenez RM, Lupták A, Vinař T, Brejová B.
BMC Bioinformatics. 2016 May 18;17(1):216. doi: 10.1186/s12859-016-1074-x.

FR3D 20120611 / WebFR3D – Find Structural Motifs in RNA 3D Structures

FR3D 20120611 / WebFR3D

:: DESCRIPTION

FR3D stands for “Find RNA 3D” and is commonly pronounced “Fred”.  It was developed to find small RNA motifs (two to 20 nucleotides) in PDB files.

WebFR3D is the online version of FR3D, a suite of Matlab programs designed to search RNA 3D structures for user specified queries.

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

 FR3D

:: MORE INFORMATION

Citation:

Michael Sarver; Craig L. Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B. Leontis.
FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures,
Journal of Mathematical Biology (2008) 56:215–252.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W50-5. doi: 10.1093/nar/gkr249. Epub 2011 Apr 22.
WebFR3D–a server for finding, aligning and analyzing recurrent RNA 3D motifs.
Petrov AI1, Zirbel CL, Leontis NB.

Fit3D v005 – Small Structural Motif Screening in Proteins and further analyses

Fit3D v005

:: DESCRIPTION

Fit3D is a command line software tool to search for small structural motifs of amino acids in target proteins. It can also be used for batch-processing by applying to a large number of target structures.

::DEVELOPER

Fit3D team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 Fit3D

:: MORE INFORMATION

Citation:

Fit3D – A web application for highly accurate screening of spatial residue patterns in protein structure data.
Kaiser F, Eisold A, Bittrich S, Labudde D.
Bioinformatics. 2015 Oct 30. pii: btv637.

SA-Mot – Extract Structural Motifs from Protein Loop Structures using HMM-SA

SA-Mot

:: DESCRIPTION

SA-Mot (Structural Alphabet Motif) is a webser allowing the extraction of motifs of interest from protein loop structures. It is composed of two steps: (i) extraction of structural motifs and (ii) the description of structural motifs.

::DEVELOPER

SA-Mot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W203-9. doi: 10.1093/nar/gkr410. Epub 2011 Jun 10.
SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.
Regad L1, Saladin A, Maupetit J, Geneix C, Camproux AC.

PatSearch – Detection of Patterns and Structural Motifs in Nucleotide Sequences

PatSearch

:: DESCRIPTION

PatSearch is a pattern matching tool for database searching of composite motifs including regular expression patterns, secondary structure elements, nucleotide weight matrices (e.g. TRANSFAC matrices)  and allowing mismatches and/or mispairings below a user-fixed threshold;

::DEVELOPER

the Research Network of Bioinformatics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences.
Grillo G, Licciulli F, Liuni S, Sbisà E, Pesole G.
Nucleic Acids Res. 2003 Jul 1;31(13):3608-12.