2005

Hart K, Nystrom B, Ohman M, Nilsson L. Molecular dynamics simulations and free energy calculations of base flipping in dsRNA. Rna 2005;11(5):609-618.

Duan J, Nilsson L. Thermal unfolding simulations of a multimeric protein--transition state and unfolding pathways. Proteins 2005;59(2):170-182.

Carlsson P, Koehler KF, Nilsson L. Glucocorticoid Receptor Point Mutation V571M Facilitates Coactivator and Ligand Binding by Structural Rearrangement and Stabilization. Mol Endocrinol 2005.

2004

Starikow EB, Nilsson L, Hulsmeyer M. A single residue exchange between two HLA-B27 alleles triggers increased peptide flexibility. Eur Biophys J 2004;33(7):651-655.

Foloppe N, Nilsson L. The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues. Structure (Camb) 2004;12(2):289-300.

Norberg J, Nilsson L. Comment on 'Free energy calculations for DNA base stacking by replica-exchange umbrella sampling' by Katsumi Murata, Yuji Sugita, Yuko Okamoto. Chem Phys Lett 2004;393(1-3):282-283.

Duan J, Nilsson L, Lambert B. Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus. Hum Mutat 2004;23(6):599-611.

2003

Norberg J, Nilsson L. Advances in biomolecular simulations: methodology and recent applications. Q Rev Biophys 2003;36(3):257-306.

Carlsson P, Nilsson L. Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling. J Comput Chem 2003;24(12):1383-1389.

Caballero-Herrera A, Nilsson L. Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus. Biophys J 2003;85(6):3646-3658.

2002

Norberg J, Nilsson L. Molecular dynamics applied to nucleic acids. Acc Chem Res 2002;35(6):465-472.

Foloppe N, Hartmann B, Nilsson L, MacKerell AD, Jr. Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J 2002;82(3):1554-1569.

Mark P, Nilsson L. Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. J Comput Chem 2002;23(13):1211-1219.

Mark P, Nilsson L. A molecular dynamics study of tryptophan in water. J Phys Chem B 2002;106(36):9440-9445.

Duan J, Nilsson L. The role of residue 50 and hydration water molecules in homeodomain DNA recognition. Eur Biophys J 2002;31(4):306-316.

Bredenberg J, Nilsson L. Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations. Proteins 2002;49(1):24-36.

2001

Sen S, Nilsson L. MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics. J Am Chem Soc 2001;123(30):7414-7422.

Mark P, Nilsson L. Molecular dynamics simulations of the Ala-Pro dipeptide in water: Conformational dynamics of trans and cis isomers using different water models. J Phys Chem B 2001;105(33):8028-8035.

Mark P, Nilsson L. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J Phys Chem A 2001;105(43):9954-9960.

Foloppe N, Nilsson L, MacKerell AD, Jr. Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics. Biopolymers 2001;61(1):61-76.

Foloppe N, Sagemark J, Nordstrand K, Berndt KD, Nilsson L. Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins. J Mol Biol 2001;310(2):449-470.

Bredenberg J, Nilsson L. Modeling zinc sulfhydryl bonds in zinc fingers. Int J Quantum Chem 2001;83(3-4):230-244.

2000

Sarzynska J, Kulinski T, Nilsson L. Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge. Biophys J 2000;79(3):1213-1227.

Norberg J, Nilsson L. On the truncation of long-range electrostatic interactions in DNA. Biophys J 2000;79(3):1537-1553.

1999

Tang Y, Nilsson L. Effect of G40R mutation on the binding of human SRY protein to DNA: a molecular dynamics view. Proteins 1999;35(1):101-113.

Tang Y, Nilsson L. Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution. Biophys J 1999;77(3):1284-1305.

Eriksson MA, Nilsson L. Structural and dynamic differences of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer to DNA: molecular dynamics simulation studies. Eur Biophys J 1999;28(2):102-111.

1998

Tang Y, Nilsson L. Interaction of human SRY protein with DNA: a molecular dynamics study. Proteins 1998;31(4):417-433.

Norberg J, Nilsson L. Solvent influence on base stacking. Biophys J 1998;74(1):394-402.

Eriksson MA, Nilsson L. Structural and dynamic effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain. Protein Eng 1998;11(7):589-600.

1996

Norberg J, Nilsson L. Conformational free energy landscape of ApApA from molecular dynamics simulations. J Phys Chem-Us 1996;100(7):2550-2554.

Norberg J, Nilsson L. Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)(2) and r(GCGCGCGCGCGC)(2). J Chem Phys 1996;104(15):6052-6057.

Norberg J, Nilsson L. Internal mobility of the oligonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations. J Biomol NMR 1996;7(4):305-314.

Norberg J, Nilsson L. Glass transition in DNA from molecular dynamics simulations. Proc Natl Acad Sci U S A 1996;93(19):10173-10176.

Norberg J, Nilsson L. Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides. Biopolymers 1996;39(6):765-768.

1995

Zilliacus J, Wright AP, Carlstedt-Duke J, Nilsson L, Gustafsson JA. Modulation of DNA-binding specificity within the nuclear receptor family by substitutions at a single amino acid position. Proteins 1995;21(1):57-67.

Vorechovsky I, Vihinen M, de Saint Basile G, Honsova S, Hammarstrom L, Muller S, Nilsson L, Fischer A, Smith CI. DNA-based mutation analysis of Bruton's tyrosine kinase gene in patients with X-linked agammaglobulinaemia. Hum Mol Genet 1995;4(1):51-58.

Vihinen M, Zvelebil MJ, Zhu Q, Brooimans RA, Ochs HD, Zegers BJ, Nilsson L, Waterfield MD, Smith CI. Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry 1995;34(5):1475-1481.

Norberg J, Nilsson L. Temperature-Dependence of the Stacking Propensity of Adenylyl-3',5'-Adenosine. J Phys Chem-Us 1995;99(35):13056-13058.

Norberg J, Nilsson L. Nmr Relaxation-Times, Dynamics, and Hydration of a Nucleic-Acid Fragment from Molecular-Dynamics Simulations. J Phys Chem-Us 1995;99(40):14876-14884.

Norberg J, Nilsson L. Stacking Free-Energy Profiles for All 16 Natural Ribodinucleoside Monophosphates in Aqueous-Solution. Journal of the American Chemical Society 1995;117(44):10832-10840.

Norberg J, Nilsson L. Potential of mean force calculations of the stacking unstacking process in single-stranded deoxyribodinucleoside monophosphates. Biophysical Journal 1995;69(6):2277-2285.

Norberg J, Nilsson L. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates. Biophys J 1995;69(6):2277-2285.

Maniar HS, Vihinen M, Webster AD, Nilsson L, Smith CI. Structural basis for X-linked agammaglobulinemia (XLA): mutations at interacting Btk residues R562, W563, and A582. Clin Immunol Immunopathol 1995;76(3 Pt 2):S198-202.

Eriksson MA, Hard T, Nilsson L. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys J 1995;68(2):402-426.

Eriksson MA, Nilsson L. Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements. Molecular dynamics simulation and free energy perturbation studies. J Mol Biol 1995;253(3):453-472.

1994

Norberg J, Nilsson L. High-Pressure Molecular-Dynamics of a Nucleic-Acid Fragment. Chem Phys Lett 1994;224(1-2):219-224.

Norberg J, Nilsson L. Stacking-Unstacking of the Dinucleoside Monophosphate Guanylyl-3',5'-Uridine Studied with Molecular-Dynamics. Biophysical Journal 1994;67(2):812-824.

Eriksson M, Hard T, Nilsson L. Molecular-Dynamics Simulation of a DNA-Binding Protein-Free and in Complex with DNA. Biophysical Journal 1994;66(2):A34-A34.