Publications

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

• General reference: [33]

• Space-filling models: applications relying on molecular models represented as unions of balls. The corresponding applications deal with interface identification and interface modeling [116], interface comparison [118], atomic packing studies [40], and coarse graining [41].

• Conformational analyses: applications dealing with conformational ensembles, sampling, and energy landscapes. In addition to various molecular distances [37], various packages are offered to explore and compare energy landscapes [42], [147], landscapes [42], compute densities of states [51], study tripeptides [odonnell2022tripeptide], design move sets for protein backbones [133], [131] .

• 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 [51], modeling molecular machines involving rigid domains connected by flexible linkers [156].

• Algorithmic packages. Various papers provide low level algorithms used in application packages, including: computing statistics on angles [44], computing the volume of a union of balls [40], comparing clustering [43] comparing high dimensional distributions [34].