NGLview–interactive molecular graphics for Jupyter notebooks

Jupyter Notebooks - a publishing format for reproducible computational workflows

It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.

Eleventh Annual Report Interactive Graphics for Molecular Graphics System

Computational Notebooks for AI Education

Computational notebooks are documents that serve dual purposes: they serve as an archive format containing code, text, images and equations; but they can also be run like computer programs. This paper explores the use of these new computational notebooks to teach AI and introduces tools that we have developed — ICalico and Calysto — to facilitate that use. Not only do these new tools broaden th...

Coot: model-building tools for molecular graphics.

CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.

Interactive Collision Detection for Molecular Graphics

Collision detection between hard-sphere representations of molecules can be performed in interactive times on existing graphics hardware. This thesis presents a system that allows a user to interactively move a small drug molecule near a larger receptor molecule and have the system immediately inform the user when a collision between the two molecules has occurred. The system uses a 3-D grid da...