SketchBio: a scientist’s 3D interface for molecular modeling and animation

  title={SketchBio: a scientist’s 3D interface for molecular modeling and animation},
  author={Shawn M. Waldon and Peter M. Thompson and Patrick J. Hahn and Russell M. Taylor},
  journal={BMC Bioinformatics},
BackgroundBecause of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations.ResultsSketchBio is presented, a tool that incorporates state-of-the-art… 

Visualization of molecular machinery using agent-based animation

This paper proposes an agent-based model for animating molecular machines, and demonstrates that agent- based animation is a viable option for molecular machines.

Bringing macromolecular machinery to life using 3D animation.

  • J. Iwasa
  • Art
    Current opinion in structural biology
  • 2015

Instant Construction and Visualization of Crowded Biological Environments

A novel set of GPU algorithms are presented that build the basis for the rapid construction of complex biological structures, consisting of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures, within an interactive visual environment.

Vision-augmented molecular dynamics simulation of nanoindentation

A user-friendly vision-augmented technique to carry out atomic simulation using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations, and the ease of carrying out molecular dynamics simulation in a more efficient way.

PyMOL mControl: Manipulating molecular visualization with mobile devices

  • W. W. LamS. Siu
  • Computer Science
    Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
  • 2017
The gesture‐based and touch‐based interaction methods to manipulate virtual objects in PyMOL utilizing the motion and touch sensors in a mobile device are designed and considered to be more suitable for oral presentations and equally suitable for education scenarios such as school classes.

Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology

This thesis proposes several novel techniques that facilitate the instant construction of mesoscale structures capable of instantly constructing large-scale biological environments using the basic structural building blocks of cells, mainly nucleic acids, lipids, and soluble proteins.

Application of Collision Detection Algorithm in 2 D Animation Design

The problems that need to be paid attention to designing the collision detection system are introduced; the current main collision detection algorithms are analyzed; and the advantages and disadvantages of the commonly used algorithms are expounded.


The development of technology today is one of the things that cannot be avoided, it actually becomes an opportunity for one of them in the field of Education. The aim of this study was to determine

Multibody dynamics analysis (MDA) as a numerical modelling tool to reconstruct the function and palaeobiology of extinct organisms

The underlying principles of MDA are provided, a number of recent studies using MDA to reconstruct the palaeobiology of fossil organisms are presented and the potential for future studies is discussed.



Design by Dragging: An Interface for Creative Forward and Inverse Design with Simulation Ensembles

We present an interface for exploring large design spaces as encountered in simulation-based engineering, design of visual effects, and other tasks that require tuning parameters of

PresentaBALL — A powerful package for presentations and lessons in structural biology

PresentaBALL enables researchers in biology with basic knowledge in HTML, JavaScript, or Python to easily setup academic tutorials, demonstrations, or scientific presentations and lectures with 3D structure content and interactive workflows.

The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voice

This is the first toolkit for macromolecular graphics that supports multiple devices with a set of controls sufficiently rich to be useful in the day-to-day work of a broad range of life scientists.

VMD: visual molecular dynamics.

UCSF Chimera—A visualization system for exploratory research and analysis

Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.

EZ‐Viz, a tool for simplifying molecular viewing in PyMOL

  • L. GrellC. ParkinLen SlatestP. Craig
  • Biology
    Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
  • 2006
A tabbed interface for PyMOL is created called EZ‐Viz, which contains a series of buttons and entry fields that allow users to select given attributes of a molecule and make changes to it by clicking a button as opposed to issuing highly syntactical commands.

The Visualization Toolkit

BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine

The model chosen to elaborate the system is Calmodulin, a protein favorite among structural and dynamic studies due to its (relative) simplicity of structure and small dimension, and a procedure that enables the building of a 'navigation map' of NMR models, that can help in the identification of movements.

Pearls found on the way to the ideal interface for scanned probe microscopes

This paper lists the particular visualization and control techniques that have enabled actual scientific discovery, including specific examples of insight gained using each technique, to help scientists determine which features are likely to be useful in their particular application and which would be just sugar coating.