Molecular docking using shape descriptors

@article{Shoichet1992MolecularDU,
  title={Molecular docking using shape descriptors},
  author={Brian K. Shoichet and Irwin D. Kuntz and Dale L. Bodian},
  journal={Journal of Computational Chemistry},
  year={1992},
  volume={13}
}
Molecular docking explores the binding modes of two interacting molecules. The technique is increasingly popular for studying protein‐ligand interactions and for drug design. A fundamental problem problem with molecular docking is that orientation space is very large and grows combinatorially with the number of degrees of freedom of the interacting molecules. Here, we describe and evaluate algorithms that improve the efficiency and accuracy of a shape‐based docking method. We use molecular… Expand

Topics from this paper

Molecular Docking: A Tool for Ligand Discovery and Design
The ability to propose reasonable ligand-receptor binding geometries is crucial to the success of structure-based drug design. One approach is to “dock” molecules together in many ways and thenExpand
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
Flexible ligand docking using conformational ensembles
TLDR
The ligand ensemble method was 100‐fold faster than docking a single conformation at a time and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation. Expand
Paper AN OVERVIEW ON MOLECULAR DOCKING
Molecular Docking is the computational modeling of the structure of complexes formed by two or more interacting molecules. The goal of molecular docking is the prediction of the three dimensionalExpand
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
Computational studies on protein-ligand docking.
This thesis describes the development and refinement of a number of techniques for molecular docking and ligand database screening, as well as the application of these techniques to predict theExpand
MOLECULAR DOCKING: A REVIEW
Molecular Docking is a study of Receptor of Protein , f it together . The problem is like solving a 3 dimensional puzzle. For example, the action of a harmful protein in h uman body may be prohibitedExpand
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.
TLDR
The four-dimensional (4D) docking approach is described that allows seamless incorporation of receptor conformational ensembles in a single docking simulation and reduces the sampling time while preserving the accuracy of traditional ensemble docking. Expand
Biased Docking for Protein-Ligand Pose Prediction.
TLDR
This work describes how to apply the AutoDock Bias protocol, a simple and elegant strategy that allows users to incorporate target-specific information through a modified scoring function that biases the ligand structure towards those poses (or conformations) that establish selected interactions. Expand
Ligand solvation in molecular docking
TLDR
Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes in a widely used molecular database, the Available Chemicals Directory. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 39 REFERENCES
Docking flexible ligands to macromolecular receptors by molecular shape.
TLDR
A method to explore the interaction of flexible ligands with receptors of known geometry on the basis of molecular shape is presented and finds binding geometries for the ligand near that observed crystallographically as well as others that provide good steric fit with the receptor. Expand
A geometric approach to macromolecule-ligand interactions.
TLDR
A method to explore geometrically feasible alignments of ligands and receptors of known structure and finds distinctly different geometries that provide good steric fits seems well-suited for generating starting conformations for energy refinement programs and interactive computer graphics routines. Expand
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.
TLDR
A method for finding a wide assortment of chemical structures that are complementary to the shape of a macromoleculer receptor site whose X-ray crystallographic structure is known and described to the binding sites of papain and carbonic anhydrase. Expand
Protein docking and complementarity.
TLDR
The ability of this docking method to regenerate the crystallographic configurations of the interacting proteins using their unbound conformations suggests that it will be a useful tool in predicting the structures of unsolved complexes. Expand
A combinatorial algorithm for calculating ligand binding
We consider the problem of predicting the mode of binding of a small molecule to a receptor site on a protein. One plausible approach, given a rigid molecule and its geometry, is to search directlyExpand
Grid‐search molecular accessible surface algorithm for solving the protein docking problem
An algorithm for solving the protein docking problem is presented. Many tentative dockings are first generated by requiring a hole on the surface of one protein to match a knob on the surface of theExpand
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.
  • P. Goodford
  • Chemistry, Medicine
  • Journal of medicinal chemistry
  • 1985
The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values. The probes include water,Expand
Computational method for the design of enzymes with altered substrate specificity.
TLDR
Using this algorithm, a protease is successfully designed that is both highly active and selective for a non-natural substrate and indicates that it is possible to design altered enzymes solely on the basis of empirical energy calculations. Expand
Molecular recognition. I. Automatic identification of topographic surface features
TLDR
An algorithm is presented that automatically finds the prominent topographic surface features of rigid α‐helices in proteins of known structure and can be reduced to a tractable problem by a docking strategy based on exhaustive trial of combinations of surface features. Expand
Protein-protein recognition: method for finding complementary surfaces of interacting proteins.
TLDR
The results obtained for the well-known autoassociation of insulin show the applicability of the method for the prediction of possible reaction modes between macromolecules. Expand
...
1
2
3
4
...