Brief introduction/tutorial for plugins.

Plugins

Plugins are graphical user interfaces with three main functions: enabling the specification of inputs, running calculations, and displaying results.

In the SBL, plugins are developed using the framework proposed in the packages Plugin_manager, which provides a coherent framework to handle targeted platforms such as PyMOL, VMD, and NGLViewer.

List of available plugins

Below is a brief overview of the currently available plugins.

Surfaces, volumes, interfaces, contacts

sbl_vorlume_pdb from the package Space_filling_model_surface_volume : computes molecular surfaces, volumes, and packing properties.

sbl_intervor_ABW_atomic from the package Space_filling_model_interface : detects pairs of interface particles, either between partners in a complex or via mediators (e.g., interfacial water molecules).

sbl_bif_chainsW_atomic from the package Space_filling_model_interface_finder : analyzes interfaces and interactions within macromolecular complexes.

sbl_misa from the package Multiple_interface_string_alignment : combines MSA with interface models to yield Multiple Interface String Alignments (MISA) that encode properties of amino acids at protein–protein interfaces.

Alignments and decompositions

sbl_kpax from the package Kpax : provides a generic implementation of the Kpax algorithm, a reference structural aligner.

sbl_spectraldom from the package Spectral_domain_explorer : identifies structural domains by maximizing intra-domain and minimizing inter-domain interactions.

Conformational analysis

sbl_tripeptide_loop_closure from the package Tripeptide_loop_closure : generates or modifies tripeptide segments using Tripeptide Loop Closure (TLC).

Structure prediction analysis

sbl_alphafold_dbrun from the package Alphafold_analysis : characterizes the fragmentation of AlphaFold predictions.

Misc

sbl_alpha_complex_of_molecular_model from the package Alpha_complex_of_molecular_model : analyzes the alpha complex of a molecular model.