Tag: 3D-motif

ASSAM / SPRITE – Side Chain 3D-motif Searching in Protein Structures

ASSAM / SPRITE

:: DESCRIPTION

The ASSAM( Amino acid Pattern Search for Substructures And Motifs) program searches for 3D patterns of amino acid side chains in PDB formatted query structures.

The SPRITE (3D Search for protein sites) server searches for protein sites and motifs in a query protein structure. The output is a list of potential functional sites.

::DEVELOPER

The Molecular Function Regulation Lab (M. Firdaus Raih research group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nadzirin et al.:
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.
Nucleic Acids Research. 2012 Jul;40(Web Server issue):W380-6.

JAR3D – Predicting RNA 3D Motifs in Sequences

JAR3D

:: DESCRIPTION

JAR3D scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
Nucleic Acids Res. 2016 May 27. pii: gkw453

Identifying novel sequence variants of RNA 3D motifs,
Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, and Neocles Leontis.
Nucleic Acids Res. 2015 Sep 3;43(15):7504-20. doi: 10.1093/nar/gkv651