• Publications
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reportedExpand
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Python: a programming language for software integration and development.
  • M. Sanner
  • Computer Science, Medicine
  • Journal of molecular graphics & modelling
  • 1 February 1999
One of the challenges in bio-computing is to enable the efficient use and inter-operation of a wide variety of rapidly-evolving computational methods to simulate, analyze, and understand the complexExpand
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Reduced surface: an efficient way to compute molecular surfaces.
Because of their wide use in molecular modeling, methods to compute molecular surfaces have received a lot of interest in recent years. However, most of the proposed algorithms compute the analyticalExpand
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Computational protein–ligand docking and virtual drug screening with the AutoDock suite
Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study ofExpand
  • 336
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A component-based software environment for visualizing large macromolecular assemblies.
  • M. Sanner
  • Medicine, Biology
  • Structure
  • 1 March 2005
The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods forExpand
  • 61
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Fast and robust computation of molecular surfaces
In this paper we define the r-reduced surface of a set of n spheres representing a molecule in relation to the r-accessible and rexchtded surfaces. Algorithms are given to compute the outer componentExpand
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AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding,Expand
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Augmented reality with tangible auto-fabricated models for molecular biology applications
The evolving technology of computer auto-fabrication ("3D printing") now makes it possible to produce physical models for complex biological molecules and assemblies. We report on an application thatExpand
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Residue-residue mean-force potentials for protein structure recognition.
We present two new sets of energy functions for protein structure recognition, given the primary sequence of amino acids along the polypeptide chain. The first set of potentials is based on theExpand
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Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS
One of the challenges in biocomputing is to enable the efficient use of a wide variety of fast-evolving computational methods to simulate, analyze, and understand the complex properties andExpand
  • 49
  • 4
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