Timeline

Max Bonomi

Head of Structure

08 Sep 2023

publication

Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence.

24 May 2023

publication

Virus Pop—Expanding Viral Databases by Protein Sequence Simulation

05 Apr 2023

publication

SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

30 May 2022

publication

Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy

20 May 2022

tool

HARIBOSS

20 May 2022

publication

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design

03 May 2022

publication

Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations

21 Apr 2022

publication

Artificial Intelligence: Exploring the conformational diversity of proteins

14 Apr 2022

publication

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.

16 Feb 2022

publication

Discovery of bat coronaviruses close to SARS-CoV-2 and infectious for human cells.

10 Sep 2021

publication

Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

08 Sep 2021

publication

Multi-replica biased sampling for photoisomerization processes in conjugated polymers

03 Mar 2021

project

Targeting RNA structure and dynamics with small molecules

03 Mar 2021

project

Integrative modelling of protein structure and dynamics with cryo-EM

03 Feb 2021

team

Computational Structural Biology

08 Oct 2020

publication

Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease

04 Feb 2020

publication

What will computational modelling approaches have to say in the era of atomistic cryo-EM data?

03 Jul 2019

tool

PLUMED-NEST

01 Jul 2019

publication

Promoting transparency and reproducibility in enhanced molecular simulations

01 Jul 2019

publication

Biomolecular Simulations: Methods and Protocols

01 Jun 2019

publication

Determination of protein structural ensembles using cryo-electron microscopy

09 May 2019

publication

Effects of α-tubulin acetylation on microtubule structure and stability

01 Feb 2019

event

Determining the structure and dynamics of biological systems using integrative approaches

24 Jan 2019

publication

A practical guide to the simultaneous determination of protein structure and dynamics using metainference

10 Jan 2019

event

CECAM school: Open source software for enhanced-sampling simulations

01 Jan 2019

publication

A Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces

01 Jan 2019

publication

Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling

23 Nov 2018

software

PLUMED

14 Nov 2018

publication

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting

02 Nov 2018

publication

A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes

06 Sep 2018

publication

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

25 Jun 2018

publication

Reversible inhibition of the ClpP protease via an N-terminal conformational switch

10 Apr 2018

publication

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

26 Mar 2018

publication

Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins

01 Jan 2018

publication

Integrative structure modeling with the Integrative Modeling Platform

15 Dec 2017

publication

Integrative structural and dynamical biology with PLUMED-ISDB

31 Oct 2017

software

Integrative Modelling Platform

16 Aug 2017

publication

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

22 Jul 2017

publication

Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide

22 Mar 2017

publication

Simultaneous quantification of protein order and disorder

05 Jan 2017

publication

Principles of protein structural ensemble determination

26 Aug 2016

publication

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

11 Mar 2016

publication

Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution

22 Jan 2016

publication

Metainference: A Bayesian inference method for heterogeneous systems

12 Nov 2015

publication

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

09 Oct 2015

publication

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

07 Oct 2015

publication

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

26 Aug 2015

publication

Specific Ion Binding at Phospholipid Membrane Surfaces

20 Aug 2015

publication

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data

01 Jan 2015

publication

Accuracy of current all-atom force-fields in modeling protein disordered states

01 Jan 2015

publication

Tackling sampling challenges in biomolecular simulations

19 Aug 2014

publication

Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data

31 Jul 2014

publication

Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ

12 Apr 2014

publication

Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone

06 Feb 2014

publication

The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery

01 Jan 2014

publication

Modeling of proteins and their assemblies with the Integrative Modeling Platform

01 Jan 2014

publication

PLUMED 2: New feathers for an old bird

18 Nov 2013

publication

Free-energy landscape of protein oligomerization from atomistic simulations

19 May 2013

publication

Structural basis for alternating access of a eukaryotic calcium/proton exchanger

03 Apr 2013

publication

Funnel metadynamics as accurate binding free-energy method

31 Mar 2013

publication

Crystal structure of a eukaryotic phosphate transporter

29 Aug 2012

publication

High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach

20 Jun 2012

publication

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

08 Jun 2011

publication

A chirality-based metrics for free-energy calculations in biomolecular systems

19 May 2011

publication

Assessing the Quality of the OPEP Coarse-Grained Force Field

01 Jan 2011

publication

Metadynamics

13 Oct 2010

publication

Multiple routes and milestones in the folding of HIV-1 protease monomer

19 May 2010

publication

Linking well-tempered metadynamics simulations with experiments

09 Mar 2010

publication

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

01 Jan 2010

publication

Enhanced sampling in the well-tempered ensemble

14 May 2009

publication

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

01 Jan 2009

publication

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

24 Sep 2008

publication

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin

15 Jun 2007

publication

A little guide for advanced search:

Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence.

Virus Pop—Expanding Viral Databases by Protein Sequence Simulation

SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy

HARIBOSS

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design

Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations

Artificial Intelligence: Exploring the conformational diversity of proteins

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.

Discovery of bat coronaviruses close to SARS-CoV-2 and infectious for human cells.

Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

Multi-replica biased sampling for photoisomerization processes in conjugated polymers

Targeting RNA structure and dynamics with small molecules

Integrative modelling of protein structure and dynamics with cryo-EM

Computational Structural Biology

Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease

What will computational modelling approaches have to say in the era of atomistic cryo-EM data?

PLUMED-NEST

Promoting transparency and reproducibility in enhanced molecular simulations

Biomolecular Simulations: Methods and Protocols

Determination of protein structural ensembles using cryo-electron microscopy

Effects of α-tubulin acetylation on microtubule structure and stability

Determining the structure and dynamics of biological systems using integrative approaches

A practical guide to the simultaneous determination of protein structure and dynamics using metainference

CECAM school: Open source software for enhanced-sampling simulations

A Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces

Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling

PLUMED

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting

A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

Reversible inhibition of the ClpP protease via an N-terminal conformational switch

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins

Integrative structure modeling with the Integrative Modeling Platform

Integrative structural and dynamical biology with PLUMED-ISDB

Integrative Modelling Platform

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide

Simultaneous quantification of protein order and disorder

Principles of protein structural ensemble determination

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution

Metainference: A Bayesian inference method for heterogeneous systems

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

Specific Ion Binding at Phospholipid Membrane Surfaces

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data

Accuracy of current all-atom force-fields in modeling protein disordered states

Tackling sampling challenges in biomolecular simulations

Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data

Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ

Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone

The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery

Modeling of proteins and their assemblies with the Integrative Modeling Platform

PLUMED 2: New feathers for an old bird

Free-energy landscape of protein oligomerization from atomistic simulations

Structural basis for alternating access of a eukaryotic calcium/proton exchanger

Funnel metadynamics as accurate binding free-energy method

Crystal structure of a eukaryotic phosphate transporter

High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

A chirality-based metrics for free-energy calculations in biomolecular systems

Assessing the Quality of the OPEP Coarse-Grained Force Field

Metadynamics

Multiple routes and milestones in the folding of HIV-1 protease monomer

Linking well-tempered metadynamics simulations with experiments

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

Enhanced sampling in the well-tempered ensemble

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin

Insight into the folding inhibition of the HIV-1 protease by a small peptide