Principles of protein-protein interactions

By Sarah A. Teichmann. European Conference on Computational Biology, 2002

1,148 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/25aed12e67018b3287242a963c8594ca846c6acd

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Vladimir N Uversky
2. Alexandre M. J. J. Bonvin
3. Lukasz Kurgan
4. David Baker
5. Yang Zhang
6. Shengyou Huang
7. Burkhard Rost
8. Jeffrey J. Gray

In Spectroscopy

1. Lukasz Kurgan
2. Vladimir N Uversky
3. Roman A. Laskowski
4. Hahnbeom Park
5. Po-Ssu Huang
6. Helen M. Berman
7. Jeffrey J. Gray
8. Chaok Seok

Citations in the corpus

• BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations (2013, background): “On the other hand, protein–protein interfaces have been shown to possess distinctive properties from core or surface regions (3–10), and the highly specific nature of many interactions established at those interfaces may be difficult to render accurately without modeling side-chain conformations at…”
• Improved prediction of protein-protein binding sites using a support vector machines approach. (2005, background): “Other interfaces have a significant number of polar residues (Jones and Thornton, 1996; Lo Conte et al., 1999; Larsen et al., 1998), usually where interactions are less permanent (Nooren and Thornton, 2003b; Glaser et al., 2001), to accommodate electrostatic interactions (Larsen et al., 1998).”
• High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design (2007, background): “37; these values are close to the average values observed for heterodimer interactions, but indicate a weaker interaction than is typical for homodimers or permanent protein complexes.(52) (b) The top 20 NMRmodels from the final AYEdes structure calculation are shown as C backbones (different color ”
• Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, positive): “4,11,12 Hu et al. 13 and Ma et al. 14 have analyzed representative families of protein–protein interfaces.”
• Analysing six types of protein-protein interfaces. (2003, background): “We introduced the term “obligomer” to denote interfaces between residues from two chains that are “obligatory” in the sense introduced by Jones & Thornton.5 In contrast, we refer to complexes as interfaces between transiently interacting chains.”
• 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 of interfaces (Jones and Thornton, 1996; Ofran and Rost, 2003a).”
• Cation–π interactions in protein–protein interfaces (2005, background): “Interfaces in weak protein complexes have, on average, lower complementarity than strong protein complexes.(8,15) Crystal-packing interfaces also have poor geometric complementarity in accordance with their inherently low specificity.”
• Reaching for high-hanging fruit in drug discovery at protein–protein interfaces (2007, background): “The contact surfaces involved in protein–protein interactions are large (∼1,500–3,000 A 2”
• Inhibiting the p53–MDM2 interaction: an important target for cancer therapy (2003, background): “The interface between both proteins is rather small (the calculated accessible surface are”
• Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions (2013, background): “1–3 Understanding the thermodynamics of protein–protein interactions is important for quantitative understanding of biological function and for enabling the design of proteins, small molecules and other compounds to modulate these interactions.”
• In silico grouping of peptide/HLA class I complexes using structural interaction characteristics (2007, methodology): “The number of intermolecular hydrogen bonds between the bound peptide and MHC protein was calculated using HBPLUS (McDonald and Thornton, 1994) in which hydrogen bonds are defined in accordance to standard geometric parameters.”
• Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners (2008, background): “Protein complexes can be formed from the association of structured proteins, by the folding of one disordered protein onto the surface of a structured partner, or by the coupled folding and binding of intrinsically disordered proteins [110-117].”
• ZRANK: Reranking protein docking predictions with an optimized energy function (2007, background): “4 There have been many exciting developments in protein–protein docking algorithms, but it is still generally performed in two sequential stages, because of the complexity of the problem.”
• Contacts-based prediction of binding affinity in protein–protein complexes (2015, background): “Interactions between proteins play a central role in the processes happening in the cells, from DNA replication to protein degradation ( Jones and Thornton, 1996 ; Alberts, 1998 ; Nooren and Thornton, 2003 ; Perkins et al., 2010 ).”