Lista de obras - Lennart Nilsson - Dominio Público Uruguay

A Molecular Dynamics Study of Tryptophan in Water

article

A comparison of15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA-binding domain

article

A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide

article

A single residue exchange between two HLA-B27 alleles triggers increased peptide flexibility

artículo científico publicado en 2004

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

artículo científico publicado en 2001

Additive CHARMM force field for naturally occurring modified ribonucleotides

artículo científico publicado en 2016

Advances in biomolecular simulations: methodology and recent applications

artículo científico publicado en 2003

Amyloid-β Peptide Targeting Peptidomimetics for Prevention of Neurotoxicity

scientific article published on 06 February 2019

CHARMM: the biomolecular simulation program

artículo científico publicado en 2009

Comment on `Free energy calculations for DNA base stacking by replica-exchange umbrella sampling' by Katsumi Murata, Yuji Sugita, Yuko Okamoto

Computational Study of Uracil Tautomeric Forms in the Ribosome: The Case of Uracil and 5-Oxyacetic Acid Uracil in the First Anticodon Position of tRNA.

artículo científico publicado en 2017

Computational studies of LXR molecular interactions reveal an allosteric communication pathway

artículo científico publicado en 2011

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields

Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.

artículo científico publicado en 2002

Crystal Structure of the HIV-2 Neutralizing Fab Fragment 7C8 with High Specificity to the V3 Region of gp125

artículo científico publicado en 2011

Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study

artículo científico publicado en 2008

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations.

artículo científico publicado en 2007

Does the dynamic Stokes shift report on slow protein hydration dynamics?

artículo científico publicado en 2009

Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima.

artículo científico publicado en 2007

Effect of Zn2+on DNA Recognition and Stability of the p53 DNA-Binding Domain†

scientific article published in 2006

Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization

artículo científico publicado en 2005

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations

artículo científico publicado en 2003

Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations

artículo científico publicado en 2012

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations

artículo científico publicado en 2009

Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics

artículo científico publicado en 2014

Fatty acids derived from royal jelly are modulators of estrogen receptor functions

artículo científico publicado en 2010

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex

artículo científico publicado en 1999

Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells

scientific article published on 14 August 2019

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization

artículo científico publicado en 2005

How thioredoxin dissociates its mixed disulfide

artículo científico publicado en 2009

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

artículo científico publicado en 2011

Implicit Solvent Models and Stabilizing Effects of Mutations and Ligands on the Unfolding of the Amyloid β-Peptide Central Helix

artículo científico publicado en 2012

Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling

artículo científico publicado en 2003

Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

artículo científico publicado en 2008

Intrinsic Relative Stabilities of the Neutral Tautomers of Arginine Side-Chain Models

article

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

artículo científico publicado en 2002

Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study

article

LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures

artículo científico publicado en 2017

Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity

artículo científico publicado en 2009

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study

artículo científico

MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics

artículo científico publicado en 2001

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

artículo científico publicado en 2012

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol

artículo científico publicado en 2010

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids

scientific article published on 23 March 2018

Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules

artículo científico publicado en 2015

Molecular dynamics applied to nucleic acids

artículo científico publicado en 2002

Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

artículo científico publicado en 2005

Molecular dynamics simulations of human LRH-1: the impact of ligand binding in a constitutively active nuclear receptor

artículo científico publicado en 2008

Molecular dynamics simulations of nucleic acid-protein complexes.

artículo científico publicado en 2008

Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus

artículo científico publicado en 2003

Molecular origin of time-dependent fluorescence shifts in proteins

artículo científico publicado en 2005

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations

artículo científico publicado en 2014

Multiple pH regime molecular dynamics simulation for pK calculations

artículo científico publicado en 2011

Mycoredoxin-1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria

artículo científico publicado en 2012

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome

artículo científico publicado en 2011

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

artículo científico publicado en 2012

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

artículo científico publicado en 2014

Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

artículo científico publicado en 1987

Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.

artículo científico publicado en 2016

Rigidity versus flexibility: the dilemma of understanding protein thermal stability

artículo científico

Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

scholarly article by Arne Elofsson published in October 1993

Sophisticated Modeling Uncovers Atomic DNA Structure in Bacteriophage Φ29 Cavity ⬇️

artículo científico publicado el 7 de mayo de 2013

Stabilization of the Catalytic Thiolate in a Mammalian Glutaredoxin: Structure, Dynamics and Electrostatics of Reduced Pig Glutaredoxin and its Mutants

article

Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif

artículo científico publicado en 2010

Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus.

artículo científico publicado en 2004

Structural effects of modified ribonucleotides and magnesium in transfer RNAs

artículo científico publicado en 2016

Structural insights into the DNA-binding specificity of E2F family transcription factors

artículo científico publicado en 2015

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

article

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

article

Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2.

artículo científico publicado en 1986

Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins

artículo científico publicado en 2001

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation

artículo científico publicado en 1999

Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia

artículo científico publicado en 2008

Structure-function defects of the twinkle amino-terminal region in progressive external ophthalmoplegia

artículo científico publicado en 2008

Synthesis and evaluation of antineurotoxicity properties of an amyloid-β peptide targeting ligand containing a triamino acid

artículo científico publicado en 2014

The -Cys-X1-X2-Cys- motif of reduced glutaredoxins adopts a consensus structure that explains the low pK(a) of its catalytic cysteine

artículo científico publicado en 2012

The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases

artículo científico publicado en 2011

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid

artículo científico publicado en 2017

The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues

artículo científico publicado en 2004

The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43.

artículo científico publicado en 2007

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

artículo científico publicado en 2006

The role of residue 50 and hydration water molecules in homeodomain DNA recognition

Thermal unfolding simulations of a multimeric protein-Transition state and unfolding pathways

scholarly article by Jianxin Duan published in February 2005

Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

Triple helical DNA in a duplex context and base pair opening

artículo científico publicado en 2014

Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics

artículo científico publicado en 2006

Understanding the -C-X1-X2-C- motif in the active site of the thioredoxin superfamily: E. coli DsbA and its mutants as a model system

artículo científico publicado en 2013

Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations

artículo científico publicado en 2011

Urea parametrization for molecular dynamics simulations

article

Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase

artículo científico publicado en 2010

Lista de obras de Lennart Nilsson

A Molecular Dynamics Study of Tryptophan in Water

A comparison of15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA-binding domain

A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide

A single residue exchange between two HLA-B27 alleles triggers increased peptide flexibility

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

Additive CHARMM force field for naturally occurring modified ribonucleotides

Advances in biomolecular simulations: methodology and recent applications

Amyloid-β Peptide Targeting Peptidomimetics for Prevention of Neurotoxicity

CHARMM: the biomolecular simulation program

Comment on `Free energy calculations for DNA base stacking by replica-exchange umbrella sampling' by Katsumi Murata, Yuji Sugita, Yuko Okamoto

Computational Study of Uracil Tautomeric Forms in the Ribosome: The Case of Uracil and 5-Oxyacetic Acid Uracil in the First Anticodon Position of tRNA.

Computational studies of LXR molecular interactions reveal an allosteric communication pathway

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields

Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.

Crystal Structure of the HIV-2 Neutralizing Fab Fragment 7C8 with High Specificity to the V3 Region of gp125

Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations.

Does the dynamic Stokes shift report on slow protein hydration dynamics?

Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima.

Effect of Zn2+on DNA Recognition and Stability of the p53 DNA-Binding Domain†

Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations

Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations

Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics

Fatty acids derived from royal jelly are modulators of estrogen receptor functions

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex

Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization

How thioredoxin dissociates its mixed disulfide

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

Implicit Solvent Models and Stabilizing Effects of Mutations and Ligands on the Unfolding of the Amyloid β-Peptide Central Helix

Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling

Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

Intrinsic Relative Stabilities of the Neutral Tautomers of Arginine Side-Chain Models

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study

LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures

Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study

MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids

Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules

Molecular dynamics applied to nucleic acids

Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

Molecular dynamics simulations of human LRH-1: the impact of ligand binding in a constitutively active nuclear receptor

Molecular dynamics simulations of nucleic acid-protein complexes.

Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus

Molecular origin of time-dependent fluorescence shifts in proteins

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations

Multiple pH regime molecular dynamics simulation for pK calculations

Mycoredoxin-1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.

Rigidity versus flexibility: the dilemma of understanding protein thermal stability

Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

Sophisticated Modeling Uncovers Atomic DNA Structure in Bacteriophage Φ29 Cavity ⬇️

Stabilization of the Catalytic Thiolate in a Mammalian Glutaredoxin: Structure, Dynamics and Electrostatics of Reduced Pig Glutaredoxin and its Mutants

Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif

Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus.

Structural effects of modified ribonucleotides and magnesium in transfer RNAs

Structural insights into the DNA-binding specificity of E2F family transcription factors

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2.

Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation

Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia

Structure-function defects of the twinkle amino-terminal region in progressive external ophthalmoplegia

Synthesis and evaluation of antineurotoxicity properties of an amyloid-β peptide targeting ligand containing a triamino acid

The -Cys-X1-X2-Cys- motif of reduced glutaredoxins adopts a consensus structure that explains the low pK(a) of its catalytic cysteine

The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid