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  1. A molecular dynamics simulation study of glycine/serine octapeptides labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene fluorophore

    Article • The Journal of Chemical Physics, April 2024, American Institute of Physics

    Danilo Roccatano

  2. Modelling the adsorption of proteins to nanoparticles at the solid-liquid interface

    Article • Journal of Colloid and Interface Science, January 2022, Elsevier

    Danilo Roccatano

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

    Article • The Journal of Physical Chemistry B, February 2019, American Chemical Society (ACS)

    Danilo Roccatano

  4. Modular assembly of proteins on nanoparticles

    Article • Nature Communications, April 2018, Springer Science + Business Media

    Danilo Roccatano

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

    Article • The Journal of Chemical Physics, February 2017, American Institute of Physics

    Danilo Roccatano

  6. Cosolvent, ions, and temperature effects on the structural properties of cecropin A-Magainin 2 hybrid peptide in solutions

    Article • Biopolymers, October 2014, Wiley

    Danilo Roccatano

  7. Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

    Article • Chemical Physics Letters, March 2014, Elsevier

    Danilo Roccatano

  8. Micellar drug nanocarriers and biomembranes: how do they interact?

    Article • Physical Chemistry Chemical Physics, January 2014, Royal Society of Chemistry

    Danilo Roccatano

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

    Article • Journal of Biotechnology, January 2014, Elsevier

    Danilo Roccatano

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

    Article • Biopolymers, December 2013, Wiley

    Danilo Roccatano

  11. Theoretical Study of Binding and Permeation of Ether-Based Polymers through Interfaces

    Article • The Journal of Physical Chemistry B, November 2013, American Chemical Society (ACS)

    Danilo Roccatano

  12. A computational protocol to predict suitable redox mediators for substitution of NAD(P)H in P450 monooxygenases

    Article • Journal of Molecular Catalysis B Enzymatic, April 2013, Elsevier

    Dr DIrk Holtmann, Danilo Roccatano

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

    Article • The Journal of Physical Chemistry B, March 2013, American Chemical Society (ACS)

    Danilo Roccatano

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

    Article • Chemical Communications, January 2013, Royal Society of Chemistry

    Danilo Roccatano

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

    Article • Journal of Chemical Theory and Computation, December 2012, American Chemical Society (ACS)

    Danilo Roccatano

  16. dRTP and dPTP a complementary nucleotide couple for the Sequence Saturation Mutagenesis (SeSaM) method

    Article • Journal of Molecular Catalysis B Enzymatic, December 2012, Elsevier

    Danilo Roccatano

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

    Article • The Journal of Physical Chemistry B, November 2012, American Chemical Society (ACS)

    Danilo Roccatano

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

    Article • Acta Crystallographica Section F Structural Biology and Crystallization Communications, August 2012, International Union of Crystallography

    Danilo Roccatano

  19. Correction to “Diffusion of 1,2-Dimethoxyethane and 1,2-Dimethoxypropane through Phosphatidycholine Bilayers: A Molecular Dynamics Study”

    Article • The Journal of Physical Chemistry B, July 2012, American Chemical Society (ACS)

    Danilo Roccatano

  20. Structure and Dynamics of Dodecaborate Clusters in Water

    Article • Inorganic Chemistry, April 2012, American Chemical Society (ACS)

    Danilo Roccatano, Prof. Dr. Detlef Gabel

  21. 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

    Article • The Journal of Chemical Physics, March 2012, American Institute of Physics

    Danilo Roccatano

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

    Article • The Journal of Physical Chemistry B, March 2012, American Chemical Society (ACS)

    Danilo Roccatano

  23. Directed Evolution of Subtilisin E into a Highly Active and Guanidinium Chloride- and Sodium Dodecylsulfate-Tolerant Protease

    Article • ChemBioChem, March 2012, Wiley

    Danilo Roccatano

  24. Validation of a hybrid MD-SCF coarse-grained model for DPPC in non-lamellar phases

    Article • Theoretical Chemistry Accounts, March 2012, Springer Science + Business Media

    Danilo Roccatano

  25. MAP2.03D: A Sequence/Structure Based Server for Protein Engineering

    Article • ACS Synthetic Biology, February 2012, American Chemical Society (ACS)

    Danilo Roccatano

  26. Directed evolution of a highly active Yersinia mollaretii phytase

    Article • Applied Microbiology and Biotechnology, December 2011, Springer Science + Business Media

    Danilo Roccatano

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

    Article • The Journal of Chemical Physics, October 2011, American Institute of Physics

    Danilo Roccatano

  28. Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

    Article • Journal of Chemical Theory and Computation, August 2011, American Chemical Society (ACS)

    Danilo Roccatano

  29. SeSaM-Tv-II Generates a Protein Sequence Space that is Unobtainable by epPCR

    Article • ChemBioChem, June 2011, Wiley

    Danilo Roccatano

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

    Article • Protein Engineering Design and Selection, April 2011, Oxford University Press (OUP)

    Danilo Roccatano

  31. Molecular Dynamics Simulation Study of Chlorophyll a in Different Organic Solvents

    Article • Journal of Chemical Theory and Computation, February 2011, American Chemical Society (ACS)

    Danilo Roccatano

  32. Study of structural and dynamic properties of liquid phenyltrimethoxysilane

    Article • Physical Chemistry Chemical Physics, January 2011, Royal Society of Chemistry

    Danilo Roccatano

  33. A Potential Antitumor Drug (Arginine Deiminase) Reengineered for Efficient Operation under Physiological Conditions

    Article • ChemBioChem, October 2010, Wiley

    Danilo Roccatano

  34. Conformational dynamics of active site loop in Escherichia coli phytase

    Article • Biopolymers, August 2010, Wiley

    Danilo Roccatano

  35. Directed Evolution of an Antitumor Drug (Arginine Deiminase PpADI) for Increased Activity at Physiological pH

    Article • ChemBioChem, February 2010, Wiley

    Danilo Roccatano

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

    Article • Protein Science, December 2008, Wiley

    Danilo Roccatano

  37. Functionalized Nanocompartments (Synthosomes) with a Reduction-Triggered Release System

    Article • Angewandte Chemie International Edition, September 2008, Wiley

    Danilo Roccatano

  38. Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions

    Article • Current Protein and Peptide Science, August 2008, Bentham Science Publishers

    Danilo Roccatano

  39. Ionic liquid effects on the activity of monooxygenase P450 BM-3

    Article • Green Chemistry, January 2008, Royal Society of Chemistry

    Dr Stefan Stolte, Danilo Roccatano

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

    Article • Biotechnology Journal, January 2008, Wiley

    Danilo Roccatano

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

    Article • Protein Engineering Design and Selection, December 2007, Oxford University Press (OUP)

    Danilo Roccatano

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

    Article • Environmental Microbiology, November 2007, Wiley

    Danilo Roccatano

  43. A 10-Å Spectroscopic Ruler Applied to Short Polyprolines

    Article • Journal of the American Chemical Society, August 2007, American Chemical Society (ACS)

    Danilo Roccatano

  44. Understanding a Mechanism of Organic Cosolvent Inactivation in Heme Monooxygenase P450 BM-3

    Article • Journal of the American Chemical Society, May 2007, American Chemical Society (ACS)

    Danilo Roccatano

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

    Article • Biopolymers, April 2007, Wiley

    Danilo Roccatano, Professor Martin Zacharias

  46. Temperature Dependence of Looping Rates in a Short Peptide

    Article • The Journal of Physical Chemistry B, March 2007, American Chemical Society (ACS)

    Danilo Roccatano, Professor Martin Zacharias

  47. Challenges of the genetic code for exploring sequence space in directed protein evolution

    Article • Biocatalysis and Biotransformation, January 2007, Taylor & Francis

    Danilo Roccatano

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

    Article • Biotechnology Journal, January 2007, Wiley

    Danilo Roccatano

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

    Article • The Journal of Physical Chemistry B, December 2006, American Chemical Society (ACS)

    Danilo Roccatano

  50. Distance Distributions of Short Polypeptides Recovered by Fluorescence Resonance Energy Transfer in the 10 Å Domain

    Article • Journal of the American Chemical Society, June 2006, American Chemical Society (ACS)

    Danilo Roccatano, Professor Martin Zacharias

  51. A Statistical Analysis of Random Mutagenesis Methods Used for Directed Protein Evolution

    Article • Journal of Molecular Biology, January 2006, Elsevier

    Danilo Roccatano, Professor Martin Zacharias

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

    Article • Biopolymers, January 2006, Wiley

    Danilo Roccatano, Professor Martin Zacharias

  53. Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study

    Article • Protein Science, October 2005, Wiley

    Danilo Roccatano, Professor Martin Zacharias

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

    Article • ChemPhysChem, August 2005, Wiley

    Danilo Roccatano

  55. Dynamical Aspects of TEM-1 β-Lactamase Probed by Molecular Dynamics

    Article • Journal of Computer-Aided Molecular Design, May 2005, Springer Science + Business Media

    Danilo Roccatano

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

    Article • ChemPhysChem, April 2005, Wiley

    Danilo Roccatano

  57. Sensitive Assay for Laboratory Evolution of Hydroxylases toward Aromatic and Heterocyclic Compounds

    Article • April 2005, SAGE Publications

    Danilo Roccatano, Professor Martin Zacharias

  58. Characterization of liquid behaviour by means of local density fluctuations

    Article • Journal of Molecular Liquids, March 2005, Elsevier

    Marco D'Abramo, Danilo Roccatano

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

    Article • Biopolymers, January 2005, Wiley

    Danilo Roccatano, Professor Martin Zacharias

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

    Article • The Journal of Physical Chemistry B, November 2004, American Chemical Society (ACS)

    Danilo Roccatano, Professor Martin Zacharias

  61. β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations

    Article • Proteins Structure Function and Bioinformatics, June 2004, Wiley

    Danilo Roccatano

  62. Investigating the Accessibility of the Closed Domain Conformation of Citrate Synthase using Essential Dynamics Sampling

    Article • Journal of Molecular Biology, June 2004, Elsevier

    Danilo Roccatano

  63. Extended Molecular Dynamics Simulation of the Carbon Monoxide Migration in Sperm Whale Myoglobin

    Article • Biophysical Journal, June 2004, Elsevier

    Danilo Roccatano

  64. Chiral discrimination in liquid 1,1,1-trifluoropropan-2-ol: A molecular dynamics study

    Article • The Journal of Chemical Physics, October 2003, American Institute of Physics

    Danilo Roccatano

  65. Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: A mechanistic study

    Article • Protein Science, March 2003, Wiley

    Danilo Roccatano

  66. Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study

    Article • Proceedings of the National Academy of Sciences, August 2002, Proceedings of the National Academy of Sciences

    Danilo Roccatano

  67. Folding and stability of the three-stranded ?-sheet peptide Betanova: Insights from molecular dynamics simulations

    Article • Proteins Structure Function and Bioinformatics, February 2002, Wiley

    Danilo Roccatano

  68. Article • Journal of Computer-Aided Molecular Design, January 2002, Springer Science + Business Media

    Danilo Roccatano

  69. Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics Simulations

    Article • The Journal of Physical Chemistry B, November 2001, American Chemical Society (ACS)

    Danilo Roccatano

  70. Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation 1 1Edited by R. Huber

    Article • Journal of Molecular Biology, July 2001, Elsevier

    Danilo Roccatano

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

    Article • Proteins Structure Function and Bioinformatics, May 1999, Wiley

    Danilo Roccatano

  72. Application of the quasi-Gaussian entropy theory to molecular dynamics simulations of Lennard-Jones fluids

    Article • The Journal of Chemical Physics, October 1998, American Institute of Physics

    Danilo Roccatano

  73. Molecular dynamics simulation of the docking of substrates to proteins

    Article • Proteins Structure Function and Bioinformatics, July 1994, Wiley

    Danilo Roccatano