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/.
| Original language | English |
|---|---|
| Journal | Nucleic Acids Research |
| Volume | 40 |
| Issue number | W1 |
| DOIs | |
| Publication status | Published - Jul 2012 |
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ASJC Scopus subject areas
- Genetics
Cite this
SPRITE and ASSAM : Web servers for side chain 3D-motif searching in protein structures. / Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Mohd Raih, Mohd Firdaus.
In: Nucleic Acids Research, Vol. 40, No. W1, 07.2012.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - SPRITE and ASSAM
T2 - Web servers for side chain 3D-motif searching in protein structures
AU - Nadzirin, Nurul
AU - Gardiner, Eleanor J.
AU - Willett, Peter
AU - Artymiuk, Peter J.
AU - Mohd Raih, Mohd Firdaus
PY - 2012/7
Y1 - 2012/7
N2 - 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/.
AB - 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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U2 - 10.1093/nar/gks401
DO - 10.1093/nar/gks401
M3 - Article
C2 - 22573174
AN - SCOPUS:84864420745
VL - 40
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - W1
ER -