BARAN, Ivan, Radka SVOBODOVÁ VAŘEKOVÁ, Laavanya PARTHASARATHI, Šimon SUCHOMEL, Fergal CASEY a Denis C. SHIELDS. Identification of potential small molecule peptidomimetics similar to motifs in proteins. Journal of Chemical Information and Modeling. 2007, roč. 47, č. 2, s. 464-474. ISSN 1549-9596.
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Základní údaje
Originální název Identification of potential small molecule peptidomimetics similar to motifs in proteins
Autoři BARAN, Ivan (703 Slovensko), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, garant, domácí), Laavanya PARTHASARATHI (372 Irsko), Šimon SUCHOMEL (203 Česká republika, domácí), Fergal CASEY (372 Irsko) a Denis C. SHIELDS (372 Irsko).
Vydání Journal of Chemical Information and Modeling, 2007, 1549-9596.
Další údaje
Originální 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: 2.986
Kód RIV RIV/00216224:14310/07:00050756
Organizační jednotka Přírodovědecká fakulta
UT WoS 000245136100021
Klíčová slova anglicky chemopeptidomics; protein structural motifs; similarity; drug molecules
Štítky AKR, rivok
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnila: Ing. Andrea Mikešková, učo 137293. Změněno: 27. 3. 2012 09:49.
Anotace
Protein-protein interactions are central to most biological processes and represent a large and important class of targets for human therapeutics. Small molecules containing peptide substituents may mimic regions of interacting proteins and inhibit their interactions. We set out to develop efficient methods to screen for similarities between known peptide structures within proteins and small molecules. We developed a method to rank peptide-compound similarities, that is restricted to small linear motifs in proteins, and to compounds containing amino acid substituents. Application to a search of the PubChem database (5.4 million compounds) using all short motifs on accessible surface areas in a nonredundant set of 11 488 peptides from the protein structure database PDB demonstrated the feasibility of the method for high throughput comparisons and the availability of compounds with comparable substituents: over 6 million compound-peptide pairs shared at least three amino acid substituents, about 100 000 of which had an rmsd score of less than 1 A. A Z-score function was developed that compares matches of a compound to different instances of the peptide motif in PDB, providing an appropriate scoring function for comparison among peptide-compound similarities involving different numbers of atoms (while simultaneously enriching for similarities that are likely to be more specific for the protein of interest). We applied the method to searches of known short protein motifs against the National Cancer Institute Developmental Therapeutic Program compound database, identifying a known true positive.
Návaznosti
LC06030, projekt VaVNázev: Biomolekulární centrum
Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum
VytisknoutZobrazeno: 2. 12. 2023 04:03