Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

@article{Gray2003ProteinproteinDW,
  title={Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.},
  author={Jeffrey J. Gray and Stewart E. Moughon and Chu Wang and Ora Schueler‐Furman and Brian Kuhlman and Carol A. Rohl and David Baker},
  journal={Journal of molecular biology},
  year={2003},
  volume={331 1},
  pages={
          281-99
        }
}
Protein-protein docking algorithms provide a means to elucidate structural details for presently unknown complexes. Here, we present and evaluate a new method to predict protein-protein complexes from the coordinates of the unbound monomer components. The method employs a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain conformations using Monte Carlo minimization. Up to 10(5) independent simulations are carried out… Expand
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  • 2007
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References

SHOWING 1-10 OF 66 REFERENCES
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.
TLDR
In terms of discriminating between docked structures, the refinement was applied to two classes of protein-protein complex: five protease-protein inhibitor and four antibody-antigen complexes, and the ability of the energy function to discriminate between native and non-native states is encouraging. Expand
Protein–protein docking with multiple residue conformations and residue substitutions
TLDR
Results suggest that sampling multiple residue conformations and residue substitutions of the unbound ligand contributes to, but does not fully provide, a solution to the protein docking problem. Expand
Soft protein–protein docking in internal coordinates
TLDR
An efficient pseudo‐Brownian rigid‐body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side‐chains is presented and can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. Expand
Protein docking along smooth association pathways
  • C. Camacho, S. Vajda
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2001
TLDR
The method accounts for the dominant driving forces at the different length scales of the protein binding process, allowing for an efficient selection of a downhill path on the evolving receptor-ligand-free energy landscape. Expand
Modelling protein docking using shape complementarity, electrostatics and biochemical information.
TLDR
A protein docking study was performed for two classes of biomolecular complexes: six enzyme/inhibitor and four antibody/antigen and tested the native rather than the complexed forms of the proteins to address the more scientifically interesting problem of predictive docking. Expand
Scoring docked conformations generated by rigid‐body protein‐protein docking
TLDR
A two‐step scoring algorithm that can discriminate near‐native conformations (with less than 5 Å RMSD) from other structures is described and developed and tested using docking decoys, i.e., docked conformations generated by Fourier correlation techniques. Expand
BiGGER: A new (soft) docking algorithm for predicting protein interactions
A new computationally efficient and automated “soft docking” algorithm is described to assist the prediction of the mode of binding between two proteins, using the three‐dimensional structures of theExpand
Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis
TLDR
The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible. Expand
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
TLDR
The key feature of the algorithm is the use of target functions that are highly tolerant to conformational changes upon binding that may provide a general solution to the unbound docking problem. Expand
Protein–protein docking predictions for the CAPRI experiment
We predicted structures for all seven targets in the CAPRI experiment using a new method in development at the time of the challenge. The technique includes a low‐resolution rigid body Monte CarloExpand
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