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Lennart Nilsson

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TOP 3
Lennart Nilsson
Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity.
Mika Ito; Jan Johansson; Roger Strömberg; Lennart Nilsson
Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations.
Lennart Nilsson; Andrey Karshikoff
Multiple pH regime molecular dynamics simulation for pK calculations.

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All Publications

2013: Lennart Nilsson
Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity.
Biophysical journal 2013;104(9):1840-1.
2012: Mika Ito; Jan Johansson; Roger Strömberg; Lennart Nilsson
Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations.
PloS one 2012;7(1):e30510.
2011: Lennart Nilsson; Andrey Karshikoff
Multiple pH regime molecular dynamics simulation for pK calculations.
PloS one 2011;6(5):e20116.
2011: Mika Ito; Jan Johansson; Roger Strömberg; Lennart Nilsson
Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations.
PloS one 2011;6(3):e17587.
2010: Marina Siponen; Magdalena Wisniewska; Lari Lehtiö; Ida Johansson; Linda Svensson; Grzegorz Raszewski; Lennart Nilsson; Mikael Sigvardsson; Helena Berglund
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.
The Journal of biological chemistry 2010;285(34):25875-9.
2010: E Jedel; Margda Waern; David Gustafson; Mikael Landén; Elias Eriksson; Göran Holm; Lennart Nilsson; A-K Lind; P O Janson; Elisabet Stener-Victorin
Anxiety and depression symptoms in women with polycystic ovary syndrome compared with controls matched for body mass index.
Human reproduction (Oxford, England) 2010;25(2):450-6.
2009: Sofia Burendahl; Cristian Danciulescu; Lennart Nilsson
Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity.
Proteins 2009;77(4):842-56.
2009: Lennart Nilsson
Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations.
Journal of computational chemistry 2009;30(9):1490-8.
2009: Bertil Halle; Lennart Nilsson
Does the dynamic Stokes shift report on slow protein hydration dynamics?
The journal of physical chemistry. B 2009;113(24):8210-3.
2009: Teresa Holmlund; Géraldine Farge; Vineet Pande; Jenny Korhonen; Lennart Nilsson; Maria Falkenberg
Structure-function defects of the twinkle amino-terminal region in progressive external ophthalmoplegia.
Biochimica et biophysica acta 2009;1792(2):132-9.
2008: Katarina Hart; Lennart Nilsson
Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study.
Proteins 2008;73(2):325-37.
2008: Boel Nyström Macchion; Roger Strömberg; Lennart Nilsson
Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes.
Journal of biomolecular structure & dynamics 2008;26(2):163-73.
2008: Sofia Burendahl; Eckardt Treuter; Lennart Nilsson
Molecular dynamics simulations of human LRH-1: the impact of ligand binding in a constitutively active nuclear receptor.
Biochemistry 2008;47(18):5205-15.
2008: Jenny A Korhonen; Vineet Pande; Teresa Holmlund; Géraldine Farge; Xuan Hoi Pham; Lennart Nilsson; Maria Falkenberg
Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia.
Journal of molecular biology 2008;377(3):691-705.
2008: Vineet Pande; Lennart Nilsson
Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.
Nucleic acids research 2008;36(5):1508-16.
2007: Nicolas Foloppe; Lennart Nilsson
Stabilization of the catalytic thiolate in a mammalian glutaredoxin: structure, dynamics and electrostatics of reduced pig glutaredoxin and its mutants.
Journal of molecular biology 2007;372(3):798-816.
2007: Cristian Danciulescu; Rudolf Ladenstein; Lennart Nilsson
Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima.
Biochemistry 2007;46(29):8537-49.
2007: Boel Nyström; Lennart Nilsson
Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs.
Journal of biomolecular structure & dynamics 2007;24(6):525-36.
2007: Pekka Mark; Lennart Nilsson
A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide.
European biophysics journal : EBJ 2007;36(3):213-24.
2006: Peter Carlsson; Sofia Burendahl; Lennart Nilsson
Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics.
Biophysical journal 2006;91(9):3151-61.
2006: Jianxin Duan; Lennart Nilsson
Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain.
Biochemistry 2006;45(24):7483-92.
2005: Lennart Nilsson; Bertil Halle
Molecular origin of time-dependent fluorescence shifts in proteins.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(39):13867-72.
2005: Ana Caballero-Herrera; Kerstin Nordstrand; Kurt D Berndt; Lennart Nilsson
Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization.
Biophysical journal 2005;89(2):842-57.
2005: Nicolas Foloppe; Lennart Nilsson
Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides.
The journal of physical chemistry. B 2005;109(18):9119-31.
2005: Jianxin Duan; Lennart Nilsson
Thermal unfolding simulations of a multimeric protein--transition state and unfolding pathways.
Proteins 2005;59(2):170-82.
2004: Jianxin Duan; Lennart Nilsson; Bo Lambert
Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus.
Human mutation 2004;23(6):599-611.
2004: Nicolas Foloppe; Lennart Nilsson
The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues.
Structure (London, England : 1993) 2004;12(2):289-300.
2003: Ana Caballero-Herrera; Lennart Nilsson
Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus.
Biophysical journal 2003;85(6):3646-58.
2003: Joanna Sarzynska; Lennart Nilsson; Tadeusz Kulinski
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.
Biophysical journal 2003;85(6):3445-59.
2003: Peter Carlsson; Lennart Nilsson
Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling.
Journal of computational chemistry 2003;24(12):1383-9.
2003: Jan Norberg; Lennart Nilsson
Advances in biomolecular simulations: methodology and recent applications.
Quarterly reviews of biophysics 2003;36(3):257-306.
2002: Johan Bredenberg; Lennart Nilsson
Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.
Proteins 2002;49(1):24-36.
2002: Pekka Mark; Lennart Nilsson
Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations.
Journal of computational chemistry 2002;23(13):1211-9.
2002: Jianxin Duan; Lennart Nilsson
The role of residue 50 and hydration water molecules in homeodomain DNA recognition.
European biophysics journal : EBJ 2002;31(4):306-16.
2002: Jan Norberg; Lennart Nilsson
Molecular dynamics applied to nucleic acids.
Accounts of chemical research 2002;35(6):465-72.
2002: Nicolas Foloppe; Brigitte Hartmann; Lennart Nilsson; Alexander D. Mackerell
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study.
Biophysical journal 2002;82(3):1554-69.
2001: Nicolas Foloppe; Johan Sagemark; Kerstin Nordstrand; Kurt D Berndt; Lennart Nilsson
Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins.
Journal of molecular biology 2001;310(2):449-70.
2000: A Lahiri; Lennart Nilsson
Molecular dynamics of the anticodon domain of yeast tRNA(Phe): codon-anticodon interaction.
Biophysical journal 2000;79(5):2276-89.
2000: Jan Norberg; Lennart Nilsson
On the truncation of long-range electrostatic interactions in DNA.
Biophysical journal 2000;79(3):1537-53.
2000: Joanna Sarzynska; Tadeusz Kulinski; Lennart Nilsson
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
Biophysical journal 2000;79(3):1213-27.
1999: S Sen; Lennart Nilsson
Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex.
Biophysical journal 1999;77(4):1801-10.
1999: S Sen; Lennart Nilsson
Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.
Biophysical journal 1999;77(4):1782-800.
1999: Y Tang; Lennart Nilsson
Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution.
Biophysical journal 1999;77(3):1284-305.
1999: Y Tang; Lennart Nilsson
Effect of G40R mutation on the binding of human SRY protein to DNA: a molecular dynamics view.
Proteins 1999;35(1):101-13.
1998: Y Tang; Lennart Nilsson
Interaction of human SRY protein with DNA: a molecular dynamics study.
Proteins 1998;31(4):417-33.
1996: J Norberg; Lennart Nilsson
Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides.
Biopolymers 1996;39(6):765-8.
1996: J Norberg; Lennart Nilsson
Glass transition in DNA from molecular dynamics simulations.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(19):10173-6.
1996: J Norberg; Lennart Nilsson
Internal mobility of the oligonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations.
Journal of biomolecular NMR 1996;7(4):305-14.
1995: M A Eriksson; Torleif Härd; Lennart Nilsson
On the pH dependence of amide proton exchange rates in proteins.
Biophysical journal 1995;69(2):329-39.
1995: Mauno Vihinen; Marketa Zvelebil; Q Zhu; R A Brooimans; H D Ochs; B J Zegers; Lennart Nilsson; M D Waterfield; C I Smith
Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia.
Biochemistry 1995;34(5):1475-81.
1994: Mauno Vihinen; David Vetrie; H S Maniar; H D Ochs; Q Zhu; Igor Vorechovský; A D Webster; L D Notarangelo; Lennart Nilsson; J M Sowadski
Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(26):12803-7.
1994: Mauno Vihinen; Lennart Nilsson; C I Smith
Structural basis of SH2 domain mutations in X-linked agammaglobulinemia.
Biochemical and biophysical research communications 1994;205(2):1270-7.
1994: J Norberg; Lennart Nilsson
Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics.
Biophysical journal 1994;67(2):812-24.