Computational methods for the prediction of protein interactions.

By Alfonso Valencia, Florencio Pazos. Current Opinion in Structural Biology, 2002

385 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a1e4f76b7959c68f7d0fbb27953561c20d040047

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Citations in the corpus

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “Furthermore, a number of algorithms have been devised that allow de novo prediction of functional links between proteins (29–32), albeit usually with considerable rates of false positives and without providing hints on the speciﬁcity and type of a predicted interaction.”
Assessing predictions of protein–protein interaction: The CAPRI experiment (2005, methodology): “Docking algorithms developed in the years 1990–2000 have often been reviewed (Smith and Sternberg 2002; Halperin et al. 2002; Valencia and Pazos 2002; Wodak and Janin 2002).”
Protein interaction networks from yeast to human. (2004, background): “fusion, neighborhood and phylogenetic profile) to predict functional relations between gene products [1–3] and the respective networks of such associations.”
STRING v10: protein–protein interaction networks, integrated over the tree of life (2014, background): “…abstracts and a large collection of full-text articles, (iv) interactions are predicted de novo by a number of algorithms using genomic information (23–25) as well as by co-expression analysis and (v) interactions that are observed in one organism are systematically transferred to other organisms,…”
Protein–protein interaction and quaternary structure (2008, background): “…proteins may be identified by searching for the co-evolution of their amino acid sequences, but the accuracy is poor unless the structure of a homologous complex is available (Pazos & Valencia, 2002 ; Valencia & Pazos, 2002 ; Mintseris & Weng, 2005 ; Halperin et al. 2006 ; Juan et al. 2008).”
Chapter 4: Protein Interactions and Disease (2012, neutral): “preserve the interaction [29,30,42–45].”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, background): “The more general problem of predicting if two proteins interact with each other has been studied extensively using a wide variety of approaches ( de Juan et al., 2013 ; Hosur et al., 2012; Zhang et al., 2012 ; Shoemaker and Panchenko, 2007 , Valencia and Pazos, 2002 , Ochoa and Pazos, 2010 ).”
Exploiting evolutionary relationships for predicting protein structures (2003, background): “…that drive their interactions (Aloy and Russell, 2002; Boulton et al., 2001; Brazhnik et al., 2002; Drewes and Bouwmeester, 2003; Gavin and Superti-Furga, 2003; Legrain et al., 2001; Robertson, 2002; Tucker et al., 2001; Valencia and Pazos, 2002; Wojcik et al., 2002; Xenarios and Eisenberg, 2001).”
Graph theory and networks in Biology. (2006, background): “…in networks with broad-tailed distributions 1In fact, the form P (k) ∼ (k + k0)−γe−k/kc with offset k0 and an exponential cutoff kc is more usually fitted to real network data. vary substantially from their mean value, and 〈k〉 cannot be thought of as a typical value for the network in this case.”
STRING 7—recent developments in the integration and prediction of protein interactions (2006, background): “Known interactions are further complemented by de novo interaction predictions derived from several comparative genomics prediction algorithms that are mainly applicable to prokaryotes (13–19).”
Predicting protein-protein interactions using signature products (2005, background): “A good overview of these and other approaches can be found in Valencia and Pazos (2002) .”