Max Bonomi

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member
team
department
center
program_project
nrc
whocc
project
software
tool
patent

Keywords

Positions

Administrative Staff
Assistant Professor
Associate Professor
Clinical Research Assistant
Clinical Research Nurse
Clinician Researcher
Department Manager
Dual-education Student
Full Professor
Honorary Professor
Lab assistant
Master Student
MD-PhD Student
Medical Staff
Non-permanent Researcher
Nursing Staff
Permanent Researcher
Pharmacist
PhD Student
Physician
Post-doc
Prize
Project Manager
Research Associate
Research Engineer
Retired scientist
Technician
Undergraduate Student
Veterinary
Visiting Scientist

Appointments

Deputy Director of Center
Deputy Director of Department
Deputy Director of National Reference Center
Deputy Head of Facility
Director of Center
Director of Department
Director of Institute
Director of National Reference Center
Group Leader
Head of Facility
Head of Operations
Head of Structure
Honorary President of the Departement
Labex Coordinator

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Pierre Lê-Bury

Maylis Lejeune

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About

I am a CNRS researcher and group leader of the “Integrative structural biology of dynamic systems” team in the “Structural Bioinformatics Unit”. For more information about my research, please visit the page of my group.

Relevant bibliography

[1] R.-A. A. Garibsingh et al. Proc. Natl. Acad. Sci. USA 118 (2021) e2104093118

[2] J. S. Fraser, K. Lindorff-Larsen, M. Bonomi. J. Chem. Inf. Model. 60 (2020) 2410

[3] The PLUMED consortium. Nat. Methods 16 (2019) 670

[4] L. Eshun-Wilson et al. Proc. Natl. Acad. Sci. USA 116 (2019) 10366

[5] M. Bonomi, R. Pellarin, M. Vendruscolo. Biophys. J. 114 (2018) 1604

[6] S. Vahidi et al. Proc. Natl. Acad. Sci. USA 115 (2018) E6447

[7] M. Bonomi, G. Heller, C. Camilloni, M. Vendruscolo. Curr. Opin. Struct. Biol. 42 (2017) 106

[8] M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo. Sci. Adv. 2 (2016) e1501177

Courses

09:00

Nov 2025

Course

Artificial Intelligence (AI) in Structural Biology hands-on workshop

Part 1. Critical use of AI for 3D structure prediction Instructors: Benjamin Bardiaux (Permanent researcher in the Bacterial Transmembrane Systems Unit at Institut Pasteur) & Ludovic Sauguet (Research director in the Architecture & Dynamics […]

Artificial Intelligence at the Institut Pasteur

Stefaniia Ivashchenko

2025-11-13 09:00:00 2025-11-13 17:00:00 Europe/Paris Artificial Intelligence (AI) in Structural Biology hands-on workshop Part 1. Critical use of AI for 3D structure prediction Instructors: Benjamin Bardiaux (Permanent researcher in the Bacterial Transmembrane Systems Unit at Institut Pasteur) & Ludovic Sauguet (Research director in the Architecture & Dynamics […] Pasteur Institute, Rue du Docteur Roux, Paris, France

09:00

Oct 2025

Course

Artificial Intelligence (AI) in Genomics hands-on workshop

Part 1. Fine-tuning biological LLMs for functional classification Intructor: Ernest Mordret (postdoctoral researcher at the Institut Pasteur) Large Language Models (LLMs) are revolutionizing biology! They capture intricate patterns within DNA and protein sequences through […]

Artificial Intelligence at the Institut Pasteur

Stefaniia Ivashchenko

2025-10-30 09:00:00 2025-10-30 17:00:00 Europe/Paris Artificial Intelligence (AI) in Genomics hands-on workshop Part 1. Fine-tuning biological LLMs for functional classification Intructor: Ernest Mordret (postdoctoral researcher at the Institut Pasteur) Large Language Models (LLMs) are revolutionizing biology! They capture intricate patterns within DNA and protein sequences through […] Pasteur Institute, Rue du Docteur Roux, Paris, France

09:00

Mar 2026

Course

AI for Life Sciences Theoretical Workshop for Pasteur PhD students

In the frame of Pasteur 2030 strategic plan which aims to advance expertise in artificial intelligence (AI) in biological research and develop a dedicated pathway to support the autonomy and growth of young scientists, […]

Stefaniia Ivashchenko

2026-03-09 09:00:00 2026-03-11 12:30:00 Europe/Paris AI for Life Sciences Theoretical Workshop for Pasteur PhD students In the frame of Pasteur 2030 strategic plan which aims to advance expertise in artificial intelligence (AI) in biological research and develop a dedicated pathway to support the autonomy and growth of young scientists, […] Pasteur Institute, Rue du Docteur Roux, Paris, France

Transversal Projects

Artificial Intelligence at the Institut Pasteur

Institut Pasteur is actively engaged in the application of artificial intelligence methods in biomedical research. In 2018, the Institute has created a Department of Computational Biology to strengthen its expertise in the analysis of […]

Projects

Project

Ongoing

3 Members

Structural and functional impacts of variants of the ADGRV1 protein, a GPCR essential for hearing and vision

Targeting RNA structure and dynamics with small molecules

Integrative modelling of protein structure and dynamics with cryo-EM

Max Bonomi (PI)

Cryo-EM has greatly expanded our understanding of the structure and function of many important biological systems. The next challenges now concern the responses to the following questions. When advanced classification techniques of single-particle images […]

Software

Ongoing

2 Members

PLUMED

Max Bonomi (PI)

PLUMED is an open-source library for free-energy calculations in molecular systems, which works together with some of the most popular molecular dynamics engines. Free-energy calculations can be performed as a function of many order […]

Software

Ongoing

3 Members

Integrative Modelling Platform

Riccardo Pellarin (PI)

IMP‘s broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. […]

Tools

Tool

Ongoing

6 Members

HARIBOSS

Max Bonomi (PI)

HARIBOSS is a database of RNA-small molecules structures retrieved from the PDB database. HARIBOSS is regularly updated with all the structures resolved by X-ray, NMR, and cryo-EM, in which ligands with drug-like properties interact […]

Tool

Ongoing

2 Members

PLUMED-NEST

Max Bonomi (PI)

PLUMED-NEST is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper. Furthermore, PLUMED-NEST […]

Former Teams

Structural Bioinformatics

CV

Professional experience

2021-Present: Institut Pasteur, Group Leader
2018-Present: Institut Pasteur and CNRS, Chargé de recherche de classe normal
2013-2018: University of Cambridge, Postdoc – Vendruscolo group
2014-2016: University of Washington, Consultant
2010-2013: University of California San Francisco, Postdoc – Sali group

Education

June 2019: Sorbonne Université, HDR (thesis available here)
2006-2010: ETH Zurich, Ph.D. – Parrinello Group
1998-2004: Universitá degli Studi di Milano – M.Sc. in Theoretical Physics

Full CV available here (updated February 2023)

ORCID ID: 0000-0002-7321-0004

Publications

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Published on: 22 Nov 2018 • Modified on: 23 Mar 2025

A little guide for advanced search:

• Computational Structural Biology

About

Courses

Artificial Intelligence (AI) in Structural Biology hands-on workshop

Artificial Intelligence (AI) in Genomics hands-on workshop

AI for Life Sciences Theoretical Workshop for Pasteur PhD students

Transversal Projects

Artificial Intelligence at the Institut Pasteur

Projects

Structural and functional impacts of variants of the ADGRV1 protein, a GPCR essential for hearing and vision

Targeting RNA structure and dynamics with small molecules

Integrative modelling of protein structure and dynamics with cryo-EM

Software

PLUMED

Integrative Modelling Platform

Tools

HARIBOSS

PLUMED-NEST

Former Teams

Structural Bioinformatics

CV

Publications