External Seminar Frédéric Cazals "The Structural Bioinformatics Library and its plugins: the power of an integrated ecosystem"
Speaker: Frédéric Cazals - INRIA Université Côte d'Azur, Algorithms-Biology-Structure, Sophia-Antipolis
Title: The Structural Bioinformatics Library and its plugins: the power of an integrated ecosystem
Abstract:
Structural Bioinformatics often requires delicate analysis of (ensembles) or structures and/or predictions. To this end, we have been developing the Structural Bioinformatics Library, a comprehensive
environment for modeling static and dynamic structures, relying on a set of coherent data structures and representations.
To ease the adoption of the proposed algorithms, we also developed a
pipeline automatically generating plugins for VMD, pymol, web servers,
etc. This ensures a minimalist development cost and a coherent user
experience across all platforms.
Plugins and the underlying command-line executables can be easily
installed on linux and Mac-OS systems using conda/pixi.
In this talk, I will present the SBL and its plugins, with demos for
various applications:
A1. Modeling and comparing protein interfaces;
A2. Assessing AlphaFold models;
A3. Generating conformational ensembles for flexible loops;
A4. Modeling dynamics of complex biomolecules involving rigid domains.
For those interested in using the SBL ecosystem, I will also help users
perform the installs and get started.
[RESOURCES AND REFERENCES]
[SBL and plugins]
* The Structural Bioinformatics Library; Bioinformatics, 2017;
doi.org/10.1093/bioinformatics/btw752; https://sbl.inria.fr/
* Plugins, list + doc: https://sbl.inria.fr/doc/sbl-plugins-guide.html
* Plugins, youtube channel: https://www.youtube.com/@SBL-Plugins
* Plugins, web servers: https://sbl.inria.fr/plugins/
[A1] Modeling protein interfaces
* Modeling Macro-Molecular Interfaces with Intervor; Bioinformatics
2010; 10.1093/bioinformatics/btq052
* Boosting the analysis of protein interfaces with Multiple Interface
String Alignment; Proteins, 2022; doi.org/10.1002/prot.26279
[A2] Assessing AlphaFold predictions
* Fold or flop: quality assessment of AlphaFold predictions on whole
proteomes; Bioinformatics Advances, 2026; doi.org/10.1093/bioadv/vbag190
* Characterizing the fragmentation of AlphaFold predictions;
Bioinformatics Advances (in press), 2026;
https://www.biorxiv.org/content/10.64898/2025.12.19.695436v2
[A3] Generating conformational ensembles for flexible loops
* Enhanced conformational exploration of protein loops, J. Comp. Chem,
2023; 10.1002/jcc.27067
[A4] Modeling dynamics of complex biomolecules involving rigid domains
* Studying dynamics without explicit dynamics: a structure-based study
of the export mechanism by AcrB; Proteins, 2021; 10.1002/prot.26012
* Motion planning in high dimensional spaces hybridizing RRT and HAR via
position-direction decoupling, Submitted, 2026;
https://inria.hal.science/hal-05646929v2
Invited by Pierre-Damien Coureux