Docking and scoring protein complexes: CAPRI 3rd Edition

  title={Docking and scoring protein complexes: CAPRI 3rd Edition},
  author={Marc F. Lensink and R M{\'e}ndez and Shoshana J. Wodak},
  journal={Proteins: Structure},
The performance of methods for predicting protein–protein interactions at the atomic scale is assessed by evaluating blind predictions performed during 2005–2007 as part of Rounds 6–12 of the community‐wide experiment on Critical Assessment of PRedicted Interactions (CAPRI). These Rounds also included a new scoring experiment, where a larger set of models contributed by the predictors was made available to groups developing scoring functions. These groups scored the uploaded set and submitted… 
Docking and scoring protein interactions: CAPRI 2009
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Docking, scoring, and affinity prediction in CAPRI
The fifth evaluation of docking and related scoring methods used in the community‐wide experiment on the Critical Assessment of Predicted Interactions (CAPRI) finds that automatic docking servers exhibit a significantly improved performance, with some servers now performing on par with predictions done by humans.
Score_set: A CAPRI benchmark for scoring protein complexes
An expanded benchmark data set for testing scoring functions is presented, which comprises the consolidated ensemble of predicted complexes made available in the CAPRI scoring experiment since its inception, and contains predicted complexes for 15 published CAPRI targets.
Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment
Results show that docking routinely yields good models of the protein-protein complexes that undergo only minor changes in conformation and associate as rigid bodies, and flexible recognition accompanying large conformation changes in the components remains difficult to simulate, and structural predictions generally yield lower quality models.
Protein-protein docking tested in blind predictions: the CAPRI experiment.
Docking algorithms build multimolecular assemblies based on the subunit structures. "Unbound" docking, which starts with the free molecules and allows for conformation changes, may be used to predict
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations, and that docking procedures tend to perform better than standard homology modeled techniques.
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
Modelling of conformational flexibility in interacting proteins remains an important area with a crucial need for improvement, and tangible progress is suggested from better integration of different modeling tools with docking procedures, as well as the use of more sophisticated evolutionary information to score models.
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment
The quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP‐CAPRI protein assembly prediction experiment indicated that residues in binding interfaces were correctly predicted in a sizable fraction of otherwise poorly modeled assemblies.
Modeling of protein complexes in CAPRI Round 37 using template‐based approach combined with model selection
The overall results show possible uses of PPI3D and VoroMQA in structural modeling of protein‐protein interactions and suggest ways for further improvements of both methods.
Scoring docking conformations using predicted protein interfaces
T-PioDock is proposed, a framework for detection of a native-like docked complex 3D structure that supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction ( T-PIP).


CAPRI: A Critical Assessment of PRedicted Interactions
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.
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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.
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 several
The targets of CAPRI rounds 6–12
Six protein–protein complexes and two homodimeric proteins involved in a variety of biological processes were offered as targets to CAPRI by crystallographers in Rounds 6–12, showing that docking methods have value even when there is an experimental structure.
Classification of protein complexes based on docking difficulty
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.
Principles of docking: An overview of search algorithms and a guide to scoring functions
The docking field has come of age, and the time is ripe to present the principles of docking, reviewing the current state of the field from both the computational and the biological points of view.
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology.
Critical assessment of methods of protein structure prediction (CASP)—Round 6
The conduct of the experiment is described, the categories of prediction included, and the evaluation and assessment procedures are outlined, and a brief summary of progress over the decade of CASP experiments is provided.
The atomic structure of protein-protein recognition sites.
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.