3D Analysis  ::  Collaborators' Software

Collaborations in software development with other labs lead sometimes to stand-alone applications, sometimes to embedded functions, sometimes to both and sometimes to neither. To the extent possible, we make software developed with RLab input available to all of you for use (MolProbity) or download within this website. For other cases, we have this page...

Below are links to other web sites, of current or past collaborators, where you can find software to which RLabours contributed. The group name is a link to a general page, typically containing software of a broader scope than our contribution. The short description about the group on this page may have more specific links.

PHENIX

The PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) group produces an integrated suite of software packages that generate structural models from crystallographic data.

Donald Lab

The Donald Lab makes a variety of their protein design and structure determination software available at their website. Of particular interest is their newest addition, the open-source protein design package OSPREY (Open Source Protein REdesign for You). Daniel Keedy of RLab fame and seeming BRDLab ubiquity contributed to the creation and application of a module therein called BRDEE (BackRub Dead-End Elimination) ( PDF). This algorithm incorporates backbone flexibility in the form of the backrub ( PDF, supplement). into the provable dead-end elimination framework for protein design. We would also like to note that the RLab strongly approves of the OSPREY acronym.