a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates.

a versatile, integrated software system for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures.

a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples.

a program for automatically plotting protein-ligand interactions.

an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.