Principles of docking: An overview of search algorithms and a guide to scoring functions

@article{Halperin2002PrinciplesOD,
  title={Principles of docking: An overview of search algorithms and a guide to scoring functions},
  author={Inbal Halperin and Buyong Ma and Haim Wolfson and Ruth Nussinov},
  journal={Proteins: Structure},
  year={2002},
  volume={47}
}
The docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the “correct” native conformation within the list of predicted docked conformations signals a near solution to the docking problem, has been replaced by the stark realization of the extreme difficulty of the next scoring… Expand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
Exploring the potential of global protein-protein docking: an overview and critical assessment of current programs for automatic ab initio docking.
TLDR
A comprehensive assessment of the 18 docking/scoring protocols of 14 global docking programs on the latest protein docking benchmark 4.0 is reviewed to provide a general guideline for the choice of an appropriate docking protocol and offer insights into the optimization and development of docking and scoring algorithms. Expand
Refinement of unbound protein docking studies using biological knowledge
TLDR
One scoring method searches the InterDom database for domains that are available in the proteins to be docked and evaluates the interaction of these domains in other complexes of known structure and the second analyzes the interface of each proposed conformation with regard to the conservation of Phe, Met, and Trp and their polar neighbor residues. Expand
ZDOCK: An initial‐stage protein‐docking algorithm
TLDR
A new scoring function for the initial stage of unbound docking is presented that combines the recently developed pairwise shape complementarity with desolvation and electrostatics and shows superior performance, especially for the antibody‐antigen category of test cases. Expand
The Comparison of Docking Search Algorithms and Scoring Functions: An Overview and Case Studies
TLDR
Content of the chapter is appropriate for public of Medicinal and Organic Chemistry as an overview of docking studies, and also for Computational Chemists at the beginning of their work as the introduction to application of molecular docking programs. Expand
Principles of flexible protein–protein docking
TLDR
The background and the principles of existing flexible protein–protein docking methods are described, focusing on the algorithms and their rational. Expand
How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials
TLDR
Nine different charge-assigning methods were sufficiently explored for molecular docking performance by using AutoDock4.2 to demonstrate that the empirical Gasteiger-Hückel charge is the most applicable in virtual screening for large database; meanwhile, the semiempirical AM1-BCC charge is practicable in lead compound optimization as well as accuratevirtual screening for small databases. Expand
Effect of Input Differences on the Results of Docking Calculations
TLDR
It was found that using the X-ray ligand conformation as docking input does not always produce the most accurate docked pose when compared with other sources of ligand input conformations. Expand
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
TLDR
Overall Glide appears to be a safe general choice for docking, while the choice of the best scoring tool remains to a larger extent system‐dependent and should be evaluated on a case‐by‐case basis. Expand
Docking to single‐domain and multiple‐domain proteins: Old and new challenges
TLDR
The sensitivity of MolFit is high, enabling it to produce reasonably accurate docking solutions when the structures undergo moderate local conformation changes upon complex formation or when the docked molecules are modeled, but the ranks of these solutions are sometimes too low to meet the requirements of CAPRI assessment. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 322 REFERENCES
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
Protein docking for low-resolution structures.
  • I. Vakser
  • Biology, Medicine
  • Protein engineering
  • 1995
TLDR
The results strongly suggest the use of the recognition procedure for docking studies where the detailed structures of the molecules are lacking, and a pronounced trend towards the correct structure of the molecular complex was clearly indicated. Expand
Rational automatic search method for stable docking models of protein and ligand.
TLDR
The docking method provides a useful tool for rational drug design and investigations of biochemical reaction mechanisms, and can accurately predict the correct docking structures, discriminating the correct model from incorrect ones. Expand
A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening.
  • H. .. Broughton
  • Chemistry, Medicine
  • Journal of molecular graphics & modelling
  • 2000
TLDR
These methods are able to match the ability of manual docking to assess likely inactivity on steric grounds and indeed to rank order ligands from a homologous series of cyclooxygenase-2 inhibitors with good correlation to their true activity. Expand
Automated docking of ligands to antibodies: methods and applications.
TLDR
The AutoDock program is presented as example of a method for flexibly docking ligands to antibodies to provide structural insights where adequate experimental information is missing, and the limits of the rigid protein treatment are indicated. Expand
Molecular docking to ensembles of protein structures.
TLDR
Two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures, and it is shown that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. Expand
Assessing energy functions for flexible docking
A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that aExpand
Assessing search strategies for flexible docking
TLDR
This work assesses the efficiency of molecular dynamics MD, Monte Ž, Carlo MC, and genetic algorithms GA for docking five representative ligand]receptor complexes and finds that MD provides structures that are, on average, lower in energy and closer to the crystallographic conformation. Expand
Structure prediction of protein complexes by an NMR-based protein docking algorithm
TLDR
A new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm is presented, which achieved an almost perfect separation between good approximations of the true complex structure and false positives. Expand
Docking of hydrophobic ligands with interaction-based matching algorithms
TLDR
The concept of multi-level interactions is introduced into the algorithms for automatic selection and placement of base fragments in the FlexX molecular docking software to improve the overall performance of FlexX significantly. Expand
...
1
2
3
4
5
...