Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures

@article{Mndez2005AssessmentOC,
  title={Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures},
  author={R M{\'e}ndez and Rapha{\"e}l Leplae and Marc F. Lensink and Shoshana J. Wodak},
  journal={Proteins: Structure},
  year={2005},
  volume={60}
}
The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional (3D) structure is reassessed by evaluating blind predictions, performed during 2003–2004 as part of Rounds 3–5 of the community‐wide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Ten newly determined structures of protein–protein complexes were used as targets for these rounds. They comprised 2 enzyme–inhibitor complexes, 2 antigen–antibody complexes… Expand
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References

SHOWING 1-10 OF 59 REFERENCES
The targets of CAPRI rounds 3–5
Ten protein–protein complexes have been offered by X‐ray crystallographers as targets for structure prediction in Rounds 3–5 of the CAPRI experiment. They illustrate molecular recognition in severalExpand
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
TLDR
The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional structure is assessed from a first major evaluation of blind predictions, which reveals genuine progress but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility. Expand
Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2
TLDR
This article describes and reviews the efforts using Hex 3.1 to predict the docking modes of the seven target protein–protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial, and describes several enhancements to the original spherical polar Fourier docking correlation algorithm. Expand
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. Expand
Successful discrimination of protein interactions
TLDR
Results from the prediction of protein complexes associated with the first Critical Assessment of PRediction of Interactions (CAPRI) experiment show that the top models predicted by the automated procedure were among the best communitywide predictions. Expand
Physicochemical and residue conservation calculations to improve the ranking of protein–protein docking solutions
TLDR
Using the free energy along with conservation information and other descriptors used in the literature for ranking docking solutions, such as shape complementarity and pair potentials, a global ranking procedure is developed that significantly improves the docking results by giving top ranks to near‐native complex structures. Expand
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
TLDR
A fast algorithm for filtering docked conformations with good surface complementarity, and ranking them based on their clustering properties, which provides good results for a number of complexes that were used as targets in the Critical Assessment of PRedictions of Interactions experiment. Expand
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
TLDR
A new method to predict protein-protein complexes from the coordinates of the unbound monomer components using a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain conformations using Monte Carlo minimization is presented. Expand
Identification of protein-protein interaction sites from docking energy landscapes.
TLDR
Protein docking simulations and analysis of the interaction energy landscapes are applied to identify protein-protein interaction sites to guide the design of mutations on the surfaces of proteins, provide geometrical details of a possible interaction, and help to annotate protein surfaces in structural proteomics. Expand
Classification of protein complexes based on docking difficulty
  • S. Vajda
  • Computer Science, Medicine
  • Proteins
  • 2005
TLDR
Results show that targets with a moderate expected difficulty were indeed predicted well by a number of groups, whereas the use of additional a priori information was necessary to obtain good results for some very difficult targets. Expand
...
1
2
3
4
5
...