Automated docking with grid‐based energy evaluation

@article{Meng1992AutomatedDW,
  title={Automated docking with grid‐based energy evaluation},
  author={Elaine C. Meng and Brian K. Shoichet and Irwin D. Kuntz},
  journal={Journal of Computational Chemistry},
  year={1992},
  volume={13}
}
The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor‐dependent terms in the potential function at points on a three‐dimensional grid. In four test cases where the components of… Expand
Efficient electrostatic solvation model for protein‐fragment docking
A method is presented for the fast evaluation of the binding energy of a protein‐small molecule complex with electrostatic solvation. It makes use of a fast preprocessing step based on the assumptionExpand
Orientational sampling and rigid‐body minimization in molecular docking
The biological activities of proteins depends on specific molecular recognition and binding. Computational methods for predicting binding modes can facilitate the discovery and design of ligands andExpand
A model binding site for testing scoring functions in molecular docking.
TLDR
Improved treatment of partial atomic charges and desolvation energies in database docking appears feasible and leads to better distinction of true ligands. Expand
Towards a critical evaluation of an empirical and volume-based solvation function for ligand docking
TLDR
Evaluating a variation of the desolvation energy model proposed by Stouten indicates that a good model to account for solvent effects is still a goal to achieve and shows an interesting ability to reduce the number of molecules with net charge -2 and -3 e among the top-scored molecules in a prospective test. Expand
A molecular mechanics/grid method for evaluation of ligand–receptor interactions
We present a computational method for prediction of the conformation of a ligand when bound to a macromolecular receptor. The method is intended for use in systems in which the approximate locationExpand
Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
TLDR
Improved the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures, and statistical analysis shows that even lower‐accuracy grid‐based energy representations can be effectively used when followed with full force field minimization. Expand
Docking small ligands in flexible binding sites
A novel procedure for docking ligands in a flexible binding site is presented. It relies on conjugate gradient minimization, during which nonbonded interactions are gradually switched on. Short MonteExpand
Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
TLDR
Methods that predict geometries of ligands binding to receptor molecules can facilitate ligand discovery and yield information on the factors governing complementarity and the HINT function may be generally useful as a scoring method in molecular docking. Expand
Molecular docking using surface complementarity
TLDR
A method is described to dock a ligand into a binding site in a protein on the basis of the complementarity of the inter‐molecular atomic contacts, which can assist in the design of improved ligands by indicating what changes in complementarity may occur as a result of the substitution of an atom in the ligand. Expand
Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design
TLDR
This work describes an implementation of a symmetry-corrected root-mean-square deviation method into the program DOCK based on the Hungarian algorithm for solving the minimum assignment problem, which dynamically assigns atom correspondence in molecules with symmetry. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 33 REFERENCES
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
A new approach to the problem of docking two molecules: The ellipsoid algorithm
TLDR
A recently developed method of constrained optimization, known as the ellipsoid algorithm, is explored as a tool for determining sterically acceptable interactions between two molecules, described by constraints on intermolecular distances. Expand
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
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
DOCKER, an interactive program for simulating protein receptor and substrate interactions
A computer graphics program written for the Evans & Sutherland Picture System 2 allows the interactive docking of a flexible polypeptide into a protein receptor of known three-dimensional structure.Expand
Computer graphics in real‐time docking with energy calculation and minimization
TLDR
A real‐time docking method using molecular graphics and high‐speed calculation of the energy of interaction between a drug and a receptor that compares well with those calculated by more orthodox means while also providing visual feedback on both molecular geometry and energy. 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
"Soft docking": matching of molecular surface cubes.
TLDR
A "cube representation" of molecular surface and volume is developed which enables the design of a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. Expand
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
TLDR
An accurate numerical method is described for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms, and it is found that charge‐solvent interactions can make large contributions to the total energy of a macromolecular system. Expand
...
1
2
3
4
...