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The atomic structure of protein-protein recognition sites.
TLDR
An analysis of the atomic structure of the recognition sites seen in 75 protein-protein complexes of known three-dimensional structure shows that atoms buried at protein- protein interfaces are close-packed like the protein interior.
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Protein–protein docking benchmark version 4.0
TLDR
The protein–protein docking benchmark is updated to include complexes that became available since the previous release, and provides 176 unbound–unbound cases that can be used for protein– protein docking method development and assessment.
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A dissection of specific and non-specific protein-protein interfaces.
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Interior and surface of monomeric proteins.
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CAPRI: A Critical Assessment of PRedicted Interactions
TLDR
The motivations for launching CAPRI, the rules that were applied to select targets and run the experiment, the results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems, and some conclusions can already be drawn.
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Principles of protein–protein recognition
TLDR
Results indicate that hydrophobicity is the major factor stabilising protein–protein association, while complementarity plays a selective role in deciding which proteins may associate.
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Surface and inside volumes in globular proteins
  • J. Janin
  • Chemistry, Biology
    Nature
  • 8 February 1979
TLDR
The study of the accessibility to solvent of amino acid residues in several proteins confirmed the early observation that polar residues are found mostly on the surface and non-polar residues mostly inside globular protein structures, but the accessibility shows systematic variations with the molecular weight.
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Protein–protein docking benchmark 2.0: An update
TLDR
A new version of the Protein–Protein Docking Benchmark is presented, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound–unbound test cases, and provides a platform for evaluating the progress of docking methods on a wide variety of targets.
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A protein–protein docking benchmark
TLDR
A nonredundant benchmark for testing protein–protein docking algorithms and should benefit the docking community not only as a large curated test set but also as a common ground for comparing different algorithms.
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Dissecting protein–protein recognition sites
TLDR
The recognition sites in 70 pairwise protein–protein complexes of known three‐dimensional structure are dissected in a set of surface patches by clustering atoms at the interface by reproducing the number and distribution of atoms within a patch.
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