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SUMMARY:External Seminar Frédéric Cazals -  INRIA\, Sophia-Antipolis - "
 The Structural Bioinformatics Library and its plugins: the power of an int
 egrated ecosystem"
DTSTART:20261120T130000Z
DTEND:20261120T150000Z
DTSTAMP:20261111T234200Z
UID:indico-event-603@indico.i2bc.paris-saclay.fr
DESCRIPTION:Speaker: Frédéric Cazals - INRIA Université Côte d'Azur\, 
 Algorithms-Biology-Structure\, Sophia-Antipolis\nhttps://team.inria.fr/abs
 /\nTitle: The Structural Bioinformatics Library and its plugins: the power
  of an integrated ecosystem\nAbstract:Structural Bioinformatics often req
 uires delicate analysis of (ensembles) or structures and/or predictions. 
  To this end\, we have been developing the Structural Bioinformatics Libr
 ary\, a comprehensiveenvironment for modeling static and dynamic structure
 s\, relying on a set of coherent data structures and representations.To e
 ase the adoption of the proposed algorithms\, we also developed apipeline 
 automatically generating plugins for VMD\, pymol\, web servers\,etc. This 
 ensures a minimalist development cost and a coherent userexperience across
  all platforms.Plugins and the underlying command-line executables can be 
 easilyinstalled on linux and Mac-OS systems using conda/pixi.In this talk\
 , I will present the SBL and its plugins\, with demos forvarious applicati
 ons:\nA1. Modeling and comparing protein interfaces\;A2. Assessing AlphaFo
 ld models\;A3. Generating conformational ensembles for flexible loops\;A4.
  Modeling dynamics of complex biomolecules involving rigid domains.\nFor t
 hose interested in using the SBL ecosystem\, I will also help usersperform
  the installs and get started.\n[RESOURCES AND REFERENCES]\n[SBL and plugi
 ns]* The Structural Bioinformatics Library\; Bioinformatics\, 2017\;doi.or
 g/10.1093/bioinformatics/btw752\; https://sbl.inria.fr/* Plugins\, list + 
 doc: https://sbl.inria.fr/doc/sbl-plugins-guide.html* Plugins\, youtube ch
 annel: https://www.youtube.com/@SBL-Plugins* Plugins\, web servers:  http
 s://sbl.inria.fr/plugins/\n[A1] Modeling protein interfaces* Modeling Macr
 o-Molecular Interfaces with Intervor\; Bioinformatics2010\; 10.1093/bioinf
 ormatics/btq052* Boosting the analysis of protein interfaces  with  Mult
 iple InterfaceString Alignment\; Proteins\, 2022\; doi.org/10.1002/prot.26
 279\n[A2] Assessing AlphaFold predictions* Fold or flop: quality assessmen
 t of AlphaFold predictions on wholeproteomes\; Bioinformatics Advances\, 2
 026\; 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\n[A3] Generating conf
 ormational ensembles for flexible loops* Enhanced conformational explorati
 on of protein loops\, J. Comp. Chem\,2023\; 10.1002/jcc.27067\n[A4] Modeli
 ng dynamics of complex biomolecules involving rigid domains* Studying dyna
 mics without explicit dynamics: a structure-based studyof the export mecha
 nism by AcrB\; Proteins\, 2021\; 10.1002/prot.26012* Motion planning in hi
 gh dimensional spaces hybridizing RRT and HAR viaposition-direction decoup
 ling\, Submitted\, 2026\;https://inria.hal.science/hal-05646929v2\nInvited
  by Pierre-Damien Coureux\n\nhttps://indico.i2bc.paris-saclay.fr/event/60
 3/
LOCATION:B26-N2-000 (I2BC CNRS Gif)
URL:https://indico.i2bc.paris-saclay.fr/event/603/
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