Publications

In the following, we provide a list of publications describing or using software components from the SBL:

• General reference: [34]

• Space-filling models: applications relying on molecular models represented as unions of balls. The corresponding applications deal with interface identification and interface modeling [117], interface comparison [119], atomic packing studies [41], and coarse graining [42].

• Conformational analyses: applications dealing with conformational ensembles, sampling, and energy landscapes. In addition to various molecular distances [38], various packages are offered to explore and compare energy landscapes [43], [149], landscapes [43], compute densities of states [52], study tripeptides [odonnell2022tripeptide], design move sets for protein backbones [135], [133] .

• Large assemblies: packages dealing with low resolution models of systems involving multiple subunits. The main application deals with connectivity inference using native mass spectrometry data [1],agarwal2015unveiling.

• Integrated analyses: analysis combining several of the tools just mentioned. In addition to MISAs, the specific tasks addressed encompass binding affinity predictions [52], modeling molecular machines involving rigid domains connected by flexible linkers [158].

• Algorithmic packages. Various papers provide low level algorithms used in application packages, including: computing statistics on angles [45], computing the volume of a union of balls [41], comparing clustering [44] comparing high dimensional distributions [35].