Analysing six types of protein-protein interfaces.

By Yanay Ofran, Burkhard Rost. Journal of Molecular Biology, 2003

426 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/04b23814427c4229bd07cfc858a07d4fdb266c36

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Citations in the corpus

Prediction‐based fingerprints of protein–protein interactions (2006, methodology): “12,13 These statistical biases and structural clues are also being used to develop methods for the prediction of protein–protein interaction (or binding) sites, even when no information about binding partners is available.”
Protein flexibility and rigidity predicted from sequence (2005, methodology): “In order to prove the significance of our findings, we used the find-self test that is applicable to related entities such as proteins.(63) This test basically”
Protein–Protein Interaction Hotspots Carved into Sequences (2007, methodology): “ISIS was trained on a nonredundant version of all transient protein–protein interfaces [27] in the PDB.”
CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK (2011, positive): “It has been shown that obligate interfaces differ considerably from transient interfaces in terms of size, shape, composition, contacts and conservation [15,16].”
Protein-Protein Interaction Detection: Methods and Analysis (2014, background): “Noncovalent contacts between the residue side chains are the basis for protein folding, protein assembly, and PPI [2].”
Protein–protein interaction and quaternary structure (2008, background): “Two-body potentials can be derived statistically by counting pairwise contacts across the interfaces (Moont et al. 1999 ; Glaser et al. 2001 ; Ofran & Rost, 2003 ; Saha et al. 2005).”
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, background): “It has been shown that interface types are significantly different in amino acid composition so that it is possible to predict the type of interaction interface from amino acid composition alone [5].”
Predict impact of single amino acid change upon protein structure (2012, methodology): “In addition, we used the following predicted structural and functional features: secondary structure [32,33] and solvent accessibility [24,25,32], protein flexibility [34], protein disorder [35-38], protein-protein interaction hotspots [39-41] and DNA-binding residues [42].”
The PredictProtein server (2003, methodology): “ISIS is a method that specifically predicts residues involved in transient, external protein–protein interactions (38,39).”
ISIS: interaction sites identified from sequence (2007, background): “This assumption has recently been challenged by several large-scale analyses which demonstrated that based on the composition of interacting residues, we can clearly distinguish between different types interfaces (Jones and Thornton, 1996; Ofran and Rost, 2003a).”
Disease-related mutations predicted to impact protein function (2012, methodology): “For many prediction methods developed in our group (protein-protein binding [24-26], protein-DNA binding [27], backbone flexibility [28]), the strength of an effect correlated with prediction strength, e.”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, positive): “6 In addition, through alanine-scanning mutagenesis, it has been found that the binding free energy is not distributed equally across these protein interfaces.”