List of works - Giorgio Colombo

3D-QSAR Assisted Design, Synthesis and Evaluation of Novobiocin Analogues.

scientific article

A Computational Assay of Estrogen Receptor α Antagonists Reveals the Key Common Structural Traits of Drugs Effectively Fighting Refractory Breast Cancers.

scientific article published on 12 January 2018

A Hamiltonian replica exchange molecular dynamics (MD) method for the study of folding, based on the analysis of the stabilization determinants of proteins.

scientific article published on 6 June 2013

A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators

scientific article

A dynamic perspective on the molecular recognition of chitooligosaccharide ligands by hevein domains.

scientific article

A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation.

scientific article published on 31 July 2008

A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35

scientific article

A protease-resistant Escherichia coli asparaginase with outstanding stability and enhanced anti-leukaemic activity in vitro.

scientific article published on 3 November 2017

A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen

scientific article

Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands.

scientific article published on 18 August 2015

Allosteric Modulators of HSP90 and HSP70: Dynamics Meets Function through Structure-Based Drug Design

article

Allosteric Regulation Points Control the Conformational Dynamics of the Molecular Chaperone Hsp90.

scientific article published on 20 September 2016

An efficient steroid pharmacophore-based strategy to identify new aromatase inhibitors.

scientific article published on 19 May 2009

Anharmonicity and Self-Similarity of the Free Energy Landscape of ProteinG

scientific article published in Physical Review Letters

Antileukemic activity of shepherdin and molecular diversity of hsp90 inhibitors.

scientific article published on August 2006

Assessment of Mutational Effects on Peptide Stability through Confinement Simulations.

scientific article published on 17 December 2015

Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies.

scientific article published on 6 May 2016

Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations

scientific article

Biochemical and computational insights into the anti-aromatase activity of natural catechol estrogens.

scientific article published on 19 February 2008

Chaperones rescue the energetic landscape of mutant CFTR at single molecule and in cell.

scientific article published on 30 August 2017

Chemo-enzymatic synthesis of (E)-2,3-diaryl-5-styryl-trans-2,3-dihydrobenzofuran-based scaffolds and their in vitro and in silico evaluation as a novel sub-family of potential allosteric modulators of the 90 kDa heat shock protein (Hsp90)

scientific article published on 01 May 2018

Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90

scientific article

Combined in silico and experimental approach for drug design: the binding mode of peptidic and non-peptidic inhibitors to hsp90 N-terminal domain.

scientific article

Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols.

scientific article published in December 2007

Computational approaches elucidate the allosteric mechanism of human aromatase inhibition: a novel possible route to Small-molecule regulation of CYP450s activities?

scientific article published on 15 September 2014

Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A

article

Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors

scientific article

Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations

scientific article (publication date: 2012)

Coupling high enzyme activity and stability: a challenging target

article

Covalent docking of selected boron-based serine beta-lactamase inhibitors

scientific article published on 13 February 2015

Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines

scientific article published on 2 November 2016

Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads.

scientific article published on 16 February 2017

Design, synthesis and biological evaluation of biphenylamide derivatives as Hsp90 C-terminal inhibitors

scientific article published on 14 October 2014

Designing Molecular Spanners to Throw in the Protein Networks

scientific article published on 30 January 2020

Designing Probes for Immunodiagnostics: Structural Insights into an Epitope Targeting Burkholderia Infections

scientific article published on 14 July 2017

Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein

scientific article published on November 2005

Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics

scientific article (preprint)

Dimerization capacities of FGF2 purified with or without heparin-affinity chromatography

scientific article

Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule

scientific article

Dynamic Diagnosis of Familial Prion Diseases Supports the β2-α2 Loop as a Universal Interference Target ⬇️

scientific article published on April 28, 2011

Dynamics-Based Discovery of Allosteric Inhibitors: Selection of New Ligands for the C-terminal Domain of Hsp90.

scientific article published on 30 August 2010

Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study

scientific article

Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations

scientific article published on 12 November 2013

Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

scientific article published on 12 September 2016

Exploiting Antigenic Diversity for Vaccine Design: THE CHLAMYDIA ArtJ PARADIGM

scientific article

Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities

scientific article published on 15 January 2014

Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology

scientific article

Fast three dimensional pharmacophore virtual screening of new potent non-steroid aromatase inhibitors.

scientific article

Flexible vs Rigid Epitope Conformations for Diagnostic- and Vaccine-Oriented Applications: Novel Insights from the Burkholderia pseudomallei BPSL2765 Pal3 Epitope.

scientific article

Folding and mis-folding of peptides and proteins: insights from molecular simulations.

scientific article

From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK

scientific article

HMGB1-carbenoxolone interactions: dynamics insights from combined nuclear magnetic resonance and molecular dynamics.

scientific article published on 3 February 2011

High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design

scientific article

How the ligand-induced reorganization of protein internal energies is coupled to conformational events

Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions ⬇️

scientific article published on March 2, 2012

Identification of a new scaffold for hsp90 C-terminal inhibition

scientific article published on 26 November 2013

Immunogenic and structural properties of the Asn-Gly-Arg (NGR) tumor neovasculature-homing motif

Impact of Mutations on NPAC Structural Dynamics: Mechanistic Insights from MD Simulations

scientific article published on 21 August 2019

Inactivation of TEM-1 by Avibactam (NXL-104): Insights from Quantum Mechanics/Molecular Mechanics Metadynamics Simulations

scientific article published on 30 July 2014

Integrating computational and chemical biology tools in the discovery of antiangiogenic small molecule ligands of FGF2 derived from endogenous inhibitors.

scientific article

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study

scientific article published on March 2003

Investigating Allostery in Molecular Recognition: Insights from a Computational Study of Multiple Antibody–Antigen Complexes

scientific article published on 02 January 2013

Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes ⬇️

scientific article published on November 24, 2010

Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors

scientific article (publication date: 2014)

Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations.

scientific article

Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90

scientific article published on 08 October 2019

Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide

scientific article

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

publication published on 12 April 2021

Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1

scientific article published on 28 December 2020

Mechanism of Helix Nucleation and Propagation: Microscopic View from Microsecond Time Scale MD Simulations

scientific article published on 01 November 2005

Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains

article

Mechanisms of Metabolite Amyloid Formation: Computational Studies for Drug Design against Metabolic Disorders

scientific article published on 15 February 2019

Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute

scientific article published on 03 March 2020

Methionine sulfoxides on prion protein Helix-3 switch on the alpha-fold destabilization required for conversion.

scientific article

Misfolding of the amyloid β-protein: A molecular dynamics study

scientific article

Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity

Modeling enzyme reactivity in organic solvents and water through computer simulations.

scientific article

Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer

scientific article

Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12–28): insights from all-atom molecular dynamics simulations

article

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations ⬇️

scientific article published on December 27, 2012

Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water

article

Molecular dynamics simulations of proteins and peptides: from folding to drug design.

scientific article published on April 2008

Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories

scientific article published in August 2008

Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition.

scientific article published on January 2009

Non-peptidic thrombospondin-1 mimics as fibroblast growth factor-2 inhibitors: an integrated strategy for the development of new antiangiogenic compounds

scientific article

Novel PARP-1 Inhibitor Scaffolds Disclosed by a Dynamic Structure-Based Pharmacophore Approach.

scientific article

Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology.

scientific article published on 26 March 2007

Peptides for Infectious Diseases: From Probe Design to Diagnostic Microarrays

scientific article published on 12 March 2019

Peptides for immunological purposes: design, strategies and applications.

scientific article published on 07 June 2013

Pharmacological enhancement of α-glucosidase by the allosteric chaperone N-acetylcysteine

scientific article published on 18 September 2012

Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping.

scientific article

Probing the hirudin-thrombin interaction by incorporation of noncoded amino acids and molecular dynamics simulation

scientific article published on November 2002

Protein design: from computer models to artificial intelligence

scientific article published on 24 May 2017

Rational Epitope Design for Protein Targeting ⬇️

scientific article published on November 15, 2012

Rational design of shepherdin, a novel anticancer agent.

scientific article

Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins

article

Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains.

scientific article

SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold

scientific article published on 19 December 2016

SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern

scientific article published on 01 September 2021

Screening Complex Biological Samples with Peptide Microarrays: The Favorable Impact of Probe Orientation via Chemoselective Immobilization Strategies on Clickable Polymeric Coatings

scientific article

Sequence Dependence of Amyloid Fibril Formation: Insights from Molecular Dynamics Simulations

article

Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia pseudomallei Flagellin

scientific article published on 29 July 2015

Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins

scientific article

Simulation of MscL gating in a bilayer under stress.

scientific article published on April 2003

Simulation of carbohydrate-protein interactions: computer-aided design of a second generation GM1 mimic.

scientific article published on February 2001

Small-Molecule Targeting of Heat Shock Protein 90 Chaperone Function: Rational Identification of a New Anticancer Lead

scientific article published on 01 December 2006

Structural Stability and Flexibility Direct the Selection of Activating Mutations in Epidermal Growth Factor Receptor Kinase

scientific article published on 10 July 2015

Structural analysis of a helical peptide unfolding pathway.

scientific article

Structural determinants of the unusual helix stability of a de novo engineered vascular endothelial growth factor (VEGF) mimicking peptide.

scientific article

Structure and Computation in Immunoreagent Design: From Diagnostics to Vaccines.

scientific article

Structure and sequence determinants of aggregation investigated with molecular dynamics.

scientific article published on January 2009

Structure determination and dynamics of peptides overlapping the catalytic hairpin of the Ras-specific GEF Cdc25(Mm).

scientific article published in October 2003

Structure elucidation and 3D solution conformation of the antibiotic enduracidin determined by NMR spectroscopy and molecular dynamics.

scientific article published in August 2005

Structure-activity relationships of linear and cyclic peptides containing the NGR tumor-homing motif

scientific article published on 7 October 2002

Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors.

scientific article

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics

scientific article published in February 2005

Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data

scientific article published on 06 June 2022

Surface energetics and protein-protein interactions: analysis and mechanistic implications

scientific article

Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides.

scientific article published in September 2003

Targeting tumor angiogenesis with TSP-1-based compounds: rational design of antiangiogenic mimetics of endogenous inhibitors ⬇️

scientific article published on November 1, 2010

The Chaperone TRAP1 As a Modulator of the Mitochondrial Adaptations in Cancer Cells.

scientific article published on 29 March 2017

The Importance of Detail: How Differences in Ligand Structures Determine Distinct Functional Responses in Integrin α v β 3

article

The Interplay between Structural Stability and Plasticity Determines Mutation Profiles and Chaperone Dependence in Protein Kinases.

scientific article published on 20 December 2017

The Structural Asymmetry of Mitochondrial Hsp90 (Trap1) Determines Fine Tuning of Functional Dynamics.

scientific article published on 10 January 2018

The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein–Protein Interactions

scientific article published on 18 March 2019

The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions

scientific article published in March 2006

The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study

scientific article

The molecular dynamics of assembly of the ubiquitous aortic medial amyloidal medin fragment

article

The structural intolerance of the PrP alpha-fold for polar substitution of the helix-3 methionines

scientific article published on 9 May 2010

Thermodynamics of β-amyloid fibril formation

Transcription factor protein interactomes reveal genetic determinants in heart disease

scientific article published in March 2022

Two amino acid substitutions within the first external loop of CCR5 induce human immunodeficiency virus-blocking antibodies in mice and chickens

scientific article published on 6 February 2008

Understanding Complex Mechanisms of Enzyme Reactivity: The Case of Limonene-1,2-Epoxide Hydrolases

Understanding the determinants of stability and folding of small globular proteins from their energetics

scientific article published on January 2004

Unraveling Energy and Dynamics Determinants to Interpret Protein Functional Plasticity: The Limonene-1,2-epoxide-hydrolase Case Study.

scientific article published on 15 March 2017

List of works by Giorgio Colombo

3D-QSAR Assisted Design, Synthesis and Evaluation of Novobiocin Analogues.

A Computational Assay of Estrogen Receptor α Antagonists Reveals the Key Common Structural Traits of Drugs Effectively Fighting Refractory Breast Cancers.

A Hamiltonian replica exchange molecular dynamics (MD) method for the study of folding, based on the analysis of the stabilization determinants of proteins.

A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators

A dynamic perspective on the molecular recognition of chitooligosaccharide ligands by hevein domains.

A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation.

A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35

A protease-resistant Escherichia coli asparaginase with outstanding stability and enhanced anti-leukaemic activity in vitro.

A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen

Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands.

Allosteric Modulators of HSP90 and HSP70: Dynamics Meets Function through Structure-Based Drug Design

Allosteric Regulation Points Control the Conformational Dynamics of the Molecular Chaperone Hsp90.

An efficient steroid pharmacophore-based strategy to identify new aromatase inhibitors.

Anharmonicity and Self-Similarity of the Free Energy Landscape of ProteinG

Antileukemic activity of shepherdin and molecular diversity of hsp90 inhibitors.

Assessment of Mutational Effects on Peptide Stability through Confinement Simulations.

Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies.

Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations

Biochemical and computational insights into the anti-aromatase activity of natural catechol estrogens.

Chaperones rescue the energetic landscape of mutant CFTR at single molecule and in cell.

Chemo-enzymatic synthesis of (E)-2,3-diaryl-5-styryl-trans-2,3-dihydrobenzofuran-based scaffolds and their in vitro and in silico evaluation as a novel sub-family of potential allosteric modulators of the 90 kDa heat shock protein (Hsp90)

Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90

Combined in silico and experimental approach for drug design: the binding mode of peptidic and non-peptidic inhibitors to hsp90 N-terminal domain.

Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols.

Computational approaches elucidate the allosteric mechanism of human aromatase inhibition: a novel possible route to Small-molecule regulation of CYP450s activities?

Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A

Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors

Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations

Coupling high enzyme activity and stability: a challenging target

Covalent docking of selected boron-based serine beta-lactamase inhibitors

Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines

Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads.

Design, synthesis and biological evaluation of biphenylamide derivatives as Hsp90 C-terminal inhibitors

Designing Molecular Spanners to Throw in the Protein Networks

Designing Probes for Immunodiagnostics: Structural Insights into an Epitope Targeting Burkholderia Infections

Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein

Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics

Dimerization capacities of FGF2 purified with or without heparin-affinity chromatography

Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule

Dynamic Diagnosis of Familial Prion Diseases Supports the β2-α2 Loop as a Universal Interference Target ⬇️

Dynamics-Based Discovery of Allosteric Inhibitors: Selection of New Ligands for the C-terminal Domain of Hsp90.

Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study

Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations

Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

Exploiting Antigenic Diversity for Vaccine Design: THE CHLAMYDIA ArtJ PARADIGM

Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities

Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology

Fast three dimensional pharmacophore virtual screening of new potent non-steroid aromatase inhibitors.

Flexible vs Rigid Epitope Conformations for Diagnostic- and Vaccine-Oriented Applications: Novel Insights from the Burkholderia pseudomallei BPSL2765 Pal3 Epitope.

Folding and mis-folding of peptides and proteins: insights from molecular simulations.

From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK

HMGB1-carbenoxolone interactions: dynamics insights from combined nuclear magnetic resonance and molecular dynamics.

High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design

How the ligand-induced reorganization of protein internal energies is coupled to conformational events

Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions ⬇️

Identification of a new scaffold for hsp90 C-terminal inhibition

Immunogenic and structural properties of the Asn-Gly-Arg (NGR) tumor neovasculature-homing motif

Impact of Mutations on NPAC Structural Dynamics: Mechanistic Insights from MD Simulations

Inactivation of TEM-1 by Avibactam (NXL-104): Insights from Quantum Mechanics/Molecular Mechanics Metadynamics Simulations

Integrating computational and chemical biology tools in the discovery of antiangiogenic small molecule ligands of FGF2 derived from endogenous inhibitors.

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study

Investigating Allostery in Molecular Recognition: Insights from a Computational Study of Multiple Antibody–Antigen Complexes

Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes ⬇️

Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors

Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations.

Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90

Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1

Mechanism of Helix Nucleation and Propagation: Microscopic View from Microsecond Time Scale MD Simulations

Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains

Mechanisms of Metabolite Amyloid Formation: Computational Studies for Drug Design against Metabolic Disorders

Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute

Methionine sulfoxides on prion protein Helix-3 switch on the alpha-fold destabilization required for conversion.

Misfolding of the amyloid β-protein: A molecular dynamics study

Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity

Modeling enzyme reactivity in organic solvents and water through computer simulations.

Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer

Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12–28): insights from all-atom molecular dynamics simulations