Napredna pretraga

Pregled bibliografske jedinice broj: 374985

Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests


Šikić, Mile; Tomić, Sanja; Vlahoviček, Kristian
Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests // Plos computational biology, 5 (2009), 1; e1000278-1 doi:10.1371/journal.pcbi.1000278 (međunarodna recenzija, članak, znanstveni)


Naslov
Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Autori
Šikić, Mile ; Tomić, Sanja ; Vlahoviček, Kristian

Izvornik
Plos computational biology (1553-734X) 5 (2009), 1; E1000278-1

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Protein – protein interactions ; sequence ; residues ; 3D protein structure ; Radnom Forest ; Classification ; protein docking

Sažetak
Identifying interaction sites in proteins provides important clues to the function of a protein, and is becoming increasingly relevant in topics like systems biology and drug discovery. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using i) a combination of sequence and structure-derived parameters ; and ii) sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and the F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with the F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modelling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.

Izvorni jezik
Engleski

Znanstvena područja
Fizika, Biologija, Računarstvo



POVEZANOST RADA


Projekt / tema
036-0362214-1987 - Modeliranje kompleksnih sustava (Branko Jeren, )
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )
119-0982913-1211 - Računalna genomika mikrobnih okoliša i bioinformatika ekstremofila (Kristian Vlahoviček, )

Ustanove
Fakultet elektrotehnike i računarstva, Zagreb,
Institut "Ruđer Bošković", Zagreb,
Prirodoslovno-matematički fakultet, Zagreb

Časopis indeksira:


  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


Citati