• Publications
  • Influence
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
TLDR
AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique. Expand
Python: a programming language for software integration and development.
  • M. Sanner
  • Computer Science, Medicine
  • Journal of molecular graphics & modelling
  • 1 February 1999
TLDR
In the laboratory, the laboratory investigates several areas, including protein-ligand docking, protein-protein docking, and complex molecular assemblies, as well as developing a number of computational tools such as molecular surfaces, phenomenological potentials, various docking and visualization programs which are used in conjunction with programs developed by others. Expand
Reduced surface: an efficient way to compute molecular surfaces.
TLDR
A program called MSMS is shown to be fast and reliable in computing molecular surfaces, which relies on the use of the reduced surface that is briefly defined here and from which the solvent-accessible and solvent-excluded surfaces are computed. Expand
Computational protein–ligand docking and virtual drug screening with the AutoDock suite
TLDR
This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. Expand
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
TLDR
Four methods of combining multiple target structures within a single grid‐based lookup table of interaction energies are tested, and two weighted average methods permit consistent and accurate ligand docking, using a singleGrid representation of the target protein structures. Expand
Tangible interfaces for structural molecular biology.
TLDR
This work has extended the molecular modeling environment, PMV, to support the fabrication of a wide variety of physical molecular models, and has adapted an augmented reality system to allow virtual 3D representations to be overlaid onto the tangible molecular models. Expand
A component-based software environment for visualizing large macromolecular assemblies.
  • M. Sanner
  • Computer Science, Medicine
  • Structure
  • 1 March 2005
TLDR
This paper presents a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python, and describes some of their features that are relevant to the visualization of large molecular assemblies. Expand
Fast and robust computation of molecular surfaces
TLDR
The r-reduced surface of a set of n spheres representing a molecule in relation to the r-accessible and rexchtded surfaces is defined and algorithms to compute the outer component and the analytical description of the corresponding r-excluded surface are given. Expand
FLIPDock: Docking flexible ligands into flexible receptors
TLDR
A novel protein–ligand docking software called FLIPDock (Flexible LIgand–Protein Docking) allowing the automated docking of flexible ligand molecules into active sites of flexible receptor molecules. Expand
Augmented reality with tangible auto-fabricated models for molecular biology applications
TLDR
An augmented reality system is adapted to allow virtual 3D representations to be overlaid onto a tangible molecular model that provides a powerful, intuitive interface for manipulating the computer models, streamlining the interface between human intent, the physical model, and the computational activity. Expand
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