Dissecting protein–protein recognition sites

By Pinak Chakrabarti, Joël Janin. Proteins: Structure, Function, and Bioinformatics, 2002

598 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c3f1026cafac6b0659e625366fca349368ce66cb

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In Materials Chemistry

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Citations in the corpus

Protein–Protein Interaction Hotspots Carved into Sequences (2007, methodology): “To the best of our knowledge, there is currently no method that was designed to identify hotspots from sequence. However, many methods attempt to use sequence or structure to identify which residues are located in the interface between proteins [”
PIPER: An FFT‐based protein docking program with pairwise potentials (2006, unknown): “This is not surprising, as analyses of protein complexes 34–37 show that the interfaces in enzyme–inhibitor and antibody–antigen complexes substantially differ.”
Protein–protein docking with a reduced protein model accounting for side‐chain flexibility (2003, methodology): “…ways to improve the scoring function used in the current approach in future studies Recent work by Janin and co-workers (Lo Conte et al. 1999; Chakrabarti and Janin 2002) indicates characteristic patterns of amino acids at and around a protein–protein interaction interface Such information…”
Protein–protein interaction and quaternary structure (2008, methodology): “Several servers, including PP at University College London, and PISA at the European Bioinformatics Institute (see Section 2.3), return the areas of the solvent accessible (ASA) and of the buried surfaces (BSA) of individual polypeptide chains, residues and atoms, when atomic coordinates are entered”
Structural analysis of B-cell epitopes in antibody:protein complexes (2012, background): “These findings aligns with the O-ring (Bogan and Thorn, 1998) theory, the recently proposed wet-rim-dry-core (Li et al., 2012) theory and the work of Chakrabarti and Janin, (2002) and Bickerton et al., (2011) for protein-protein interactions in general suggesting that the core of the interface…”
Analysing six types of protein-protein interfaces. (2003, background): “Chakrabarti & Janin take an approach similar to that of Bogan & Thorn,(12) and differentiate between the core of the interface and its rim.(24) They find tryptophan and tyrosine to be over-represented in the core, and leucine and valine to be under-represented.”
Recent progress and future directions in protein-protein docking. (2008, background): “These results indicate that, perhaps with the help of some prior knowledge, it is straight-forward for many current algorithms to make good docking predictions when the interface area of the complex is large and when the conformational differences between the unbound and bound structures are small.”