Applications:

For end-users, the SBL provides binary programs that can be run from the command-line. To ease the process of using them, the SBL also provides plugins for the most popular molecular visualization tools: Visual Molecular Dynamics (VMD) and PyMOL. The SBL also provides Jupyter Notebook files for each Application, available from each User Manual. See Applications: Work Packages and Installation from Pre-compiled Static Programs for more details.

Direct Access

Space Filling Models

Molecular surfaces, volumes and packing	Finding interfaces	Dissecting interfaces
Notebook	Notebook	Notebook
Interactive demo	Interactive demo (Chains) Interactive demo (Domains)	Interactive demo
Designing coarse grain models	Shelling diagrams: encoding	Shelling diagrams: comparison
	Interactive demo

Conformational Analysis

Landscape explorer	Conformational ensemble analysis	Conformational ensembles comparison
Notebook	Notebook	Notebook
Transition graphs	Energy landscape analysis	Energy landscapes comparison
Notebook	Notebook	Notebook
Molecular distances flexible	Structural motifs
Notebook	Notebook

Large Assemblies

Connectivity inference

Integrated Analysis

Binding affinity prediction	FunChaT
Multiple Interface String Alignments	Molecular cradle
Notebook	Notebook

Data Management

XML data parsing and analysis	Managing multiple runs
	Notebook

Data Analysis

Density difference based clustering

Notebook

Toolbox

Structural alignments	Clustering	3D Rigid registration
	Notebook
Morse theory for landscapes	Optimal transportation for graphs	Molecular distances
D Family matching	Protein representation	Iterative alignment
Notebook