List of works - Danilo Roccatano

A 10-A spectroscopic ruler applied to short polyprolines

scientific article

A potential antitumor drug (arginine deiminase) reengineered for efficient operation under physiological conditions

scientific article published on November 2010

A statistical analysis of random mutagenesis methods used for directed protein evolution.

scientific article

Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study

scientific article published in February 2017

Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain.

scientific article

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

scientific article

Computational study of the catalytic domain of human neutrophil collagenase. specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor.

scientific article published in March 2002

Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions.

scientific article published on August 2008

Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3.

scientific article published on 20 December 2012

Conformational and Electronic Properties of a Microperoxidase in Aqueous Solution: A Computational Study

scientific article published on 01 April 2005

Conformational dynamics of active site loop in Escherichia coli phytase.

scientific article published on November 2010

Diffusion of 1,2-Dimethoxyethane and 1,2-Dimethoxypropane through Phosphatidycholine Bilayers: A Molecular Dynamics Study

article

Directed evolution of an antitumor drug (arginine deiminase PpADI) for increased activity at physiological pH.

scientific article published in March 2010

Directed evolution of subtilisin E into a highly active and guanidinium chloride- and sodium dodecylsulfate-tolerant protease

scholarly article by Zhenwei Li published in March 2012

Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain

scientific article published in June 2006

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.

scientific article published in May 1999

Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics

scientific article published in May 2005

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

scientific article

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin

scientific article published on June 2004

Free Energy Profile of Domain Movement in Ligand-Free Citrate Synthase

scientific article published on 20 February 2019

Functionalized nanocompartments (synthosomes) with a reduction-triggered release system

scientific article

Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

article

Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations

scientific article published in March 2014

Insights on activity and stability of subtilisin E towards guanidinium chloride and sodium dodecylsulfate

scientific article published on 23 November 2013

Interaction of Curcumin with PEO–PPO–PEO Block Copolymers: A Molecular Dynamics Study

article

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

scientific article published on March 2003

Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling.

scientific article

Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation

scientific article

Laboratory evolution of P450 BM3 for mediated electron transfer yielding an activity-improved and reductase-independent variant

scientific article

MAP(2.0)3D: a sequence/structure based server for protein engineering

scientific article

Micellar drug nanocarriers and biomembranes: how do they interact?

scientific article published on 01 March 2014

Modular assembly of proteins on nanoparticles.

scientific article published on 16 April 2018

Molecular Dynamics Simulation Study of Chlorophyll a in Different Organic Solvents

scientific article published on 24 February 2011

Molecular Dynamics Simulation of Water Near Nanostructured Hydrophobic Surfaces: Interfacial Energies

article

Molecular dynamics simulation of the docking of substrates to proteins.

scientific article published in July 1994

Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates.

scientific article published on November 2004

Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents.

scientific article

P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation

scientific article

Sensitive assay for laboratory evolution of hydroxylases toward aromatic and heterocyclic compounds.

scientific article

Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries

scientific article

Structural and Dynamic Properties of the CAGQW Peptide in Water: A Molecular Dynamics Simulation Study Using Different Force Fields

article

Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture

scientific article published in August 2005

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation

scientific article published in April 2007

Structure and Dynamics of Dodecaborate Clusters in Water

article

Structure and dynamics of 1,2-dimethoxyethane and 1,2-dimethoxypropane in aqueous and non-aqueous solutions: A molecular dynamics study

article

Study of structural and dynamic properties of liquid phenyltrimethoxysilane

scientific article published on 27 May 2011

Synthetic Polymers and Biomembranes. How Do They Interact?: Atomistic Molecular Dynamics Simulation Study of PEO in Contact with a DMPC Lipid Bilayer

article

Temperature dependence of looping rates in a short peptide

scientific article published on 16 February 2007

Temperature effects on structure and dynamics of the psychrophilic protease subtilisin S41 and its thermostable mutants in solution

article

The role of active-site Phe87 in modulating the organic co-solvent tolerance of cytochrome P450 BM3 monooxygenase

scientific article

Theoretical study of binding and permeation of ether-based polymers through interfaces.

scientific article

Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study

scientific article published in December 2006

Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): a random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR.

scientific article

Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450 BM-3

scientific article

Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer Using Coarse-Grained Molecular Dynamics Simulations

article

List of works by Danilo Roccatano

A 10-A spectroscopic ruler applied to short polyprolines

A potential antitumor drug (arginine deiminase) reengineered for efficient operation under physiological conditions

A statistical analysis of random mutagenesis methods used for directed protein evolution.

Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study

Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain.

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

Computational study of the catalytic domain of human neutrophil collagenase. specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor.

Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions.

Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3.

Conformational and Electronic Properties of a Microperoxidase in Aqueous Solution: A Computational Study

Conformational dynamics of active site loop in Escherichia coli phytase.

Diffusion of 1,2-Dimethoxyethane and 1,2-Dimethoxypropane through Phosphatidycholine Bilayers: A Molecular Dynamics Study

Directed evolution of an antitumor drug (arginine deiminase PpADI) for increased activity at physiological pH.

Directed evolution of subtilisin E into a highly active and guanidinium chloride- and sodium dodecylsulfate-tolerant protease

Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.

Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics

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

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin

Free Energy Profile of Domain Movement in Ligand-Free Citrate Synthase

Functionalized nanocompartments (synthosomes) with a reduction-triggered release system

Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations

Insights on activity and stability of subtilisin E towards guanidinium chloride and sodium dodecylsulfate

Interaction of Curcumin with PEO–PPO–PEO Block Copolymers: A Molecular Dynamics Study

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

Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling.

Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation

Laboratory evolution of P450 BM3 for mediated electron transfer yielding an activity-improved and reductase-independent variant

MAP(2.0)3D: a sequence/structure based server for protein engineering

Micellar drug nanocarriers and biomembranes: how do they interact?

Modular assembly of proteins on nanoparticles.

Molecular Dynamics Simulation Study of Chlorophyll a in Different Organic Solvents

Molecular Dynamics Simulation of Water Near Nanostructured Hydrophobic Surfaces: Interfacial Energies

Molecular dynamics simulation of the docking of substrates to proteins.

Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates.

Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents.

P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation

Sensitive assay for laboratory evolution of hydroxylases toward aromatic and heterocyclic compounds.

Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries

Structural and Dynamic Properties of the CAGQW Peptide in Water: A Molecular Dynamics Simulation Study Using Different Force Fields

Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation

Structure and Dynamics of Dodecaborate Clusters in Water

Structure and dynamics of 1,2-dimethoxyethane and 1,2-dimethoxypropane in aqueous and non-aqueous solutions: A molecular dynamics study

Study of structural and dynamic properties of liquid phenyltrimethoxysilane

Synthetic Polymers and Biomembranes. How Do They Interact?: Atomistic Molecular Dynamics Simulation Study of PEO in Contact with a DMPC Lipid Bilayer

Temperature dependence of looping rates in a short peptide

Temperature effects on structure and dynamics of the psychrophilic protease subtilisin S41 and its thermostable mutants in solution

The role of active-site Phe87 in modulating the organic co-solvent tolerance of cytochrome P450 BM3 monooxygenase

Theoretical study of binding and permeation of ether-based polymers through interfaces.

Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study

Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): a random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR.

Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450 BM-3

Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer Using Coarse-Grained Molecular Dynamics Simulations