SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.

Nucleic Acids Research
Nurul NadzirinMohd Firdaus-Raih

Abstract

Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/.

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Citations

Feb 20, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Florian KaiserDirk Labudde
May 16, 2015·Nucleic Acids Research·Frédéric GuyonPierre Tufféry
Apr 20, 2016·Journal of Cheminformatics·Gabriel Núñez-VivancoMiguel Reyes-Parada
Nov 13, 2014·Bioinformatics·Sandro C IzidoroGisele L Pappa
Sep 13, 2017·Scientific Reports·Amira JabraniValérie Biou
Aug 5, 2016·Molecular Informatics·Valerie J GilletPeter Willett
May 2, 2017·Nucleic Acids Research·João P A MoraesSandro C Izidoro
Jul 3, 2019·International Journal of Molecular Sciences·Alejandro Valdés-JiménezMiguel Reyes-Parada
Dec 8, 2020·PLoS Computational Biology·Sebastian BittrichAlexander S Rose
Mar 21, 2021·Communications Biology·Nur Zazarina RamlyDavid W Rice
Mar 10, 2021·Protein Science : a Publication of the Protein Society·Israel SilmanLev Weiner
May 24, 2021·Nucleic Acids Research·Luca PinziGiulio Rastelli
Nov 9, 2017·Journal of Chemical Information and Modeling·Luca Belmonte, Sheref S Mansy
Aug 28, 2021·International Journal of Molecular Sciences·Reeki EmrizalMohd Firdaus-Raih
Jul 10, 2015··Anisio M. LacerdaSandro Izidoro

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Methods Mentioned

BETA
SPRITE
X-ray

Software Mentioned

ASSAM
GIRAF
JESS
CCP4
MegaMotifBase
RIGOR
RASMOT - 3D PRO
Jmol
Mot
SA

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