autoPACK, cellPACK

“pack any recipe of objects into anything”. Tools for assembling large-scale models from molecular building blocks.


Interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Computational capabilities include fitting molecules in maps, morphing between maps, structural superimposition, structure/sequence conservation mapping, surface electrostatics/analysis, H-bond analysis, distance/area/ volumetric analysis etc. etc. PDB format output.

Visual Molecular Dynamics (VMD)

Molecular visualization – displaying/animating and analyzing large biomolecular assemblies using 3-D graphics and scripting. Capable of working with very large structures, long-timescale simulation trajectories to be loaded into physical memory, large volumetric datasets (e.g. The 64 million atom HIV capsid simulation, Nature 2013).

Open Babel

Chemical toolbox designed to speak the many languages of chemical data. Search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Read, write and convert over 110 chemical file formats.


Tool to handle multiple aliases used to refer to the same protein. “Multiple aliases” is a common obstacle to an efficient workflow.


Comprehensive repository of biomedical ontologies. 48 resources. Advanced search and mappings. Visualization.

Gene Ontology

The Gene Ontology project aims to produce an unambiguous, universal language to describe biological phenomena across all species.