Web server to identify similarity of amino acid motifs to
compounds (SAAMCO)

J 2008

Web server to identify similarity of amino acid motifs to compounds (SAAMCO)

CASEY, Fergal P., Norman E DAVEY, Ivan BARAN, Radka SVOBODOVÁ VAŘEKOVÁ, Denis C SHIELDS et. al.

Základní údaje

Originální název

Web server to identify similarity of amino acid motifs to compounds (SAAMCO)

Autoři

CASEY, Fergal P. (372 Irsko), Norman E DAVEY (372 Irsko), Ivan BARAN (703 Slovensko), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, garant, domácí) a Denis C SHIELDS (372 Irsko)

Vydání

Journal of Chemical Information and Modeling, 2008, 1549-9596

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 3.643

Kód RIV

RIV/00216224:14310/08:00056467

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000258004300021

Klíčová slova anglicky

amino acid motifs; proteins; similarity; web server; chemopeptidomics

Štítky

Pb, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 3. 2012 03:50, doc. RNDr. Radka Svobodová, Ph.D.

Anotace

V originále

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth and signalling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide’s structure but are not compromised by poor pharmacological properties. SAAMCO is a web service that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favourable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are pre-processed and fast regular expression searches filter potential matches before time- intensive 3D superposition is performed. The required input information is minimal and the compound databases have been selected to maximize the availability of information on biological activity. “Hits” are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.

Návaznosti

LC06030, projekt VaV

Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

CASEY, Fergal P., Norman E DAVEY, Ivan BARAN, Radka SVOBODOVÁ VAŘEKOVÁ a Denis C SHIELDS. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). Journal of Chemical Information and Modeling. 2008, roč. 48, č. 7, s. 1524–1529. ISSN 1549-9596.

@article{976956,
   author = {Casey, Fergal P. and Davey, Norman E and Baran, Ivan and Svobodová Vařeková, Radka and Shields, Denis C},
   article_number = {7},
   keywords = {amino acid motifs; proteins; similarity; web server; chemopeptidomics},
   language = {eng},
   issn = {1549-9596},
   journal = {Journal of Chemical Information and Modeling},
   title = {Web server to identify similarity of amino acid motifs to compounds (SAAMCO)},
   volume = {48},
   year = {2008}
}

TY  - JOUR
ID  - 976956
AU  - Casey, Fergal P. - Davey, Norman E - Baran, Ivan - Svobodová Vařeková, Radka - Shields, Denis C
PY  - 2008
TI  - Web server to identify similarity of amino acid motifs to compounds (SAAMCO)
JF  - Journal of Chemical Information and Modeling
VL  - 48
IS  - 7
SP  - 1524–1529
EP  - 1524–1529
SN  - 15499596
KW  - amino acid motifs
KW  - proteins
KW  - similarity
KW  - web server
KW  - chemopeptidomics
N2  - Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth and signalling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide’s structure but are not compromised by poor pharmacological properties. SAAMCO is a web service that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favourable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are pre-processed and fast regular expression searches filter potential matches before time- intensive 3D superposition is performed. The required input information is minimal and the compound databases have been selected to maximize the availability of information on biological activity. “Hits” are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.
ER  -

CASEY, Fergal P., Norman E DAVEY, Ivan BARAN, Radka SVOBODOVÁ VAŘEKOVÁ a Denis C SHIELDS. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). \textit{Journal of Chemical Information and Modeling}. 2008, roč.~48, č.~7, s.~1524–1529. ISSN~1549-9596.

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