List of works - Jozica Dolenc

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

scientific article

A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents

scientific article

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution

scientific article published on 07 January 2012

Biomolecular simulation: historical picture and future perspectives.

scientific article published on February 2008

Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding

scientific article

Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data

scientific article published on 25 March 2019

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

scientific article

Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase.

scientific article published in June 2013

Exploring the Conserved Water Site and Hydration of a Coiled‐Coil Trimerisation Motif: A MD Simulation Study

scientific article published on 01 July 2008

Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements

scientific article

GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories

scientific article published on 16 September 2011

Influence of stereoregularity of the polymer chain on interactions with surfactants: binding of cetylpyridinium chloride by isotactic and atactic poly(methacrylic acid)

scientific article published on 01 May 2006

Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion

scientific article

Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

scientific article

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

scientific article

Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA

scientific article published on 01 September 2010

Molecular simulation as an aid to experimentalists.

scientific article published on 14 February 2008

Multi-resolution simulation of biomolecular systems: a review of methodological issues

scientific article published on 18 February 2013

On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters

scientific article published on 01 January 2014

On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water

scientific article

Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

scientific article published on 30 July 2012

Structure and Conformational Dynamics of the Domain 5 RNA Hairpin of a Bacterial Group II Intron Revealed by Solution Nuclear Magnetic Resonance and Molecular Dynamics Simulations

article

Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids.

scientific article published on 16 February 2015

List of works by Jozica Dolenc

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution

Biomolecular simulation: historical picture and future perspectives.

Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding

Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase.

Exploring the Conserved Water Site and Hydration of a Coiled‐Coil Trimerisation Motif: A MD Simulation Study

Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements

GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories

Influence of stereoregularity of the polymer chain on interactions with surfactants: binding of cetylpyridinium chloride by isotactic and atactic poly(methacrylic acid)

Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion

Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA

Molecular simulation as an aid to experimentalists.

Multi-resolution simulation of biomolecular systems: a review of methodological issues

On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters

On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water

Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

Structure and Conformational Dynamics of the Domain 5 RNA Hairpin of a Bacterial Group II Intron Revealed by Solution Nuclear Magnetic Resonance and Molecular Dynamics Simulations

Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids.