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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
TLDR
The incremental construction and the random search strategy are evaluated as database docking techniques with a database of 51 molecules docked to two of the crystallographic testcases and are fast enough to reliably rank the database of compounds within 15 s per molecule on an SGI R10000 cpu.
Automated docking with grid‐based energy evaluation
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
Development and validation of a modular, extensible docking program: DOCK 5
TLDR
The sampling algorithm is generally sufficient for the binding pose prediction problem for up to 7 rotatable bonds and could be improved through more advanced modeling of the receptor prior to docking and through improvement of the force field parameters, particularly for structures containing metal-based cofactors.
DOCK 6: Impact of new features and current docking performance
This manuscript presents the latest algorithmic and methodological developments to the structure‐based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection
DOCK 6: combining techniques to model RNA-small molecule complexes.
TLDR
A test set of RNA-ligand complexes is compiled to validate the ability of the DOCK suite of programs to successfully recreate experimentally determined binding poses and indicates that DOCK can indeed be useful for structure-based drug design aimed at RNA.
Structure-Based Strategies for Drug Design and Discovery
TLDR
The combination of molecular structure determination and computation is emerging as an important tool for drug development and will be applied to acquired immunodeficiency syndrome (AIDS) and bacterial drug resistance.
Molecular recognition and docking algorithms.
TLDR
This review focuses on methodological developments relevant to the field of molecular docking, and summarizes several critical methodological issues that must be addressed in future developments.
Critical evaluation of search algorithms for automated molecular docking and database screening
TLDR
It is shown that the site point–directed search is tenfold faster than a random search, but that the single graph matching algorithm boosts the speed of database screening up to 60‐fold.
The maximal affinity of ligands.
TLDR
An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands.
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