List of works - Cecilia Clementi

A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures

scientific article published on 5 December 2017

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

scientific article

A new perspective on transition states: χ1 separatrix

scientific article published in July 2011

A tripodal peptide ligand for asymmetric Rh(ii) catalysis highlights unique features of on-bead catalyst development

article

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations

scientific article published on 02 March 2019

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

scientific article

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

scientific article published on February 2010

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes

scientific article

Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment

scientific article

Coarse graining molecular dynamics with graph neural networks

scientific article published on 01 November 2020

Coarse-grained models of protein folding: toy models or predictive tools?

scientific article published on 21 December 2007

Coarse-graining molecular systems by spectral matching

scientific article published on 01 July 2019

Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods

scientific article

Combining experimental and simulation data of molecular processes via augmented Markov models.

scientific article published on 17 July 2017

Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

scientific article published on 01 December 2010

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling

scientific article

Deep learning to decompose macromolecules into independent Markovian domains

scientific article published in 2022

Delineation of folding pathways of a β-sheet miniprotein

scientific article published on 17 October 2011

Determination of reaction coordinates via locally scaled diffusion map.

scientific article published in March 2011

Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions

scientific article published on 04 January 2013

Extensible and Scalable Adaptive Sampling on Supercomputers

scientific article published on 10 November 2020

Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

scientific article published on 01 June 2007

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

scientific article published in September 2014

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

scientific article

Hamiltonian dynamics of homopolymer chain models

scientific article published on 06 October 2006

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L

scientific article published on 01 February 2003

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

scientific article published on 18 November 2015

Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype

scientific article

Kinetic distance and kinetic maps from molecular dynamics simulation

scientific article published on 11 September 2015

Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests

scientific article published on 22 July 2020

Learning Effective Molecular Models from Experimental Observables

scientific article published on 13 June 2018

Localizing Frustration in Proteins Using All-Atom Energy Functions

scientific article published on 16 May 2019

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

scholarly article

Machine Learning for Molecular Simulation

scientific article published on 24 February 2020

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

scientific article published on 15 April 2019

Machine learning for protein folding and dynamics

scientific article published on 24 December 2019

Mapping folding energy landscapes with theory and experiment

scientific article published on 29 August 2007

Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes

scientific article published on 12 November 2020

Minimalist protein model as a diagnostic tool for misfolding and aggregation

scientific article published on 03 August 2006

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

scientific article published on 01 January 2008

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.

scientific article published in October 2006

Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile

scientific article published on October 2013

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble

scientific article

Multiscale characterization of protein conformational ensembles

scientific article published on September 2009

Nanoscale coupling of endocytic pit growth and stability

scientific article published on 27 November 2019

On the characterization of protein native state ensembles

scientific article published on 8 December 2006

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

scientific article published in October 2004

Path integral-GC-AdResS simulation of a large hydrophobic solute in water: a tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space

scientific article published on 9 May 2017

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science

scientific article published on 01 November 2018

Polymer reversal rate calculated via locally scaled diffusion map.

scientific article published in April 2011

Preface: Special Topic on Reaction Pathways

scientific article

Publisher's Note: “Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile” [].

scientific article published on 9 December 2013

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

scientific article published in July 2004

Quantitative comparison of adaptive sampling methods for protein dynamics

scientific article published on 01 December 2018

Rapid Calculation of Molecular Kinetics Using Compressed Sensing.

scientific article published on 16 April 2018

Rapid exploration of configuration space with diffusion-map-directed molecular dynamics

scientific article published on 7 August 2013

Restriction versus guidance in protein structure prediction.

scientific article

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

article

Size and topology modulate the effects of frustration in protein folding

scientific article published on 27 August 2018

Sparse learning of stochastic dynamical equations

scientific article published on 01 June 2018

Structure prediction of protein-ligand complexes from sequence information with Umol

scientific article published in 2024

Supersymmetric Langevin equation to explore free-energy landscapes.

scientific article published on 26 April 2007

The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family

scientific article published on 16 October 2018

The effects of nonnative interactions on protein folding rates: theory and simulation

scientific article

The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates

scientific article

TorchMD: A Deep Learning Framework for Molecular Simulations

scientific article published on 17 March 2021

Unfolding the fold of cyclic cysteine-rich peptides

scientific article

List of works by Cecilia Clementi

A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

A new perspective on transition states: χ1 separatrix

A tripodal peptide ligand for asymmetric Rh(ii) catalysis highlights unique features of on-bead catalyst development

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes

Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment

Coarse graining molecular dynamics with graph neural networks

Coarse-grained models of protein folding: toy models or predictive tools?

Coarse-graining molecular systems by spectral matching

Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods

Combining experimental and simulation data of molecular processes via augmented Markov models.

Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling

Deep learning to decompose macromolecules into independent Markovian domains

Delineation of folding pathways of a β-sheet miniprotein

Determination of reaction coordinates via locally scaled diffusion map.

Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions

Extensible and Scalable Adaptive Sampling on Supercomputers

Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

Hamiltonian dynamics of homopolymer chain models

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype

Kinetic distance and kinetic maps from molecular dynamics simulation

Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests

Learning Effective Molecular Models from Experimental Observables

Localizing Frustration in Proteins Using All-Atom Energy Functions

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

Machine Learning for Molecular Simulation

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

Machine learning for protein folding and dynamics

Mapping folding energy landscapes with theory and experiment

Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes

Minimalist protein model as a diagnostic tool for misfolding and aggregation

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.

Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble

Multiscale characterization of protein conformational ensembles

Nanoscale coupling of endocytic pit growth and stability

On the characterization of protein native state ensembles

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

Path integral-GC-AdResS simulation of a large hydrophobic solute in water: a tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science

Polymer reversal rate calculated via locally scaled diffusion map.

Preface: Special Topic on Reaction Pathways

Publisher's Note: “Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile” [].

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

Quantitative comparison of adaptive sampling methods for protein dynamics

Rapid Calculation of Molecular Kinetics Using Compressed Sensing.

Rapid exploration of configuration space with diffusion-map-directed molecular dynamics

Restriction versus guidance in protein structure prediction.

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

Size and topology modulate the effects of frustration in protein folding

Sparse learning of stochastic dynamical equations

Structure prediction of protein-ligand complexes from sequence information with Umol

Supersymmetric Langevin equation to explore free-energy landscapes.

The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family

The effects of nonnative interactions on protein folding rates: theory and simulation

The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates

TorchMD: A Deep Learning Framework for Molecular Simulations

Unfolding the fold of cyclic cysteine-rich peptides