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About me

For more information see my Swedish page

Commmisions of trust

  • Deputy head of department, Dept. of Biosciences and Nutrition, 2013-
  • Member of the Board of Doctoral Education, Karolinska Institutet (2012 - )
  • Member of the management group of the Dept. of Biosciences and Nutrition,  KI (2009-)
  • Chairman of the National committee for molecular biosciences of KVA (2003-2013), Secretary (2014-)
  • Vice-President (2008-2010) and President (2010-2012) of the Int. Soc. for Quantum Biology and Pharmacology
  • Secretary (1996-2000), member (2000-2003) of  Europ. Biophys. Soc. Assoc. Exec. Comm.
  • Secretary (1980-1992), Chairman (1992-1995), Board member (2004-2011) of the Swed. Bioph. Soc.

Education

Civ.ing, KTH-F, 1976

TeknD, teoretisk fysik, KTH, 1983

Postdoc, Harvard University, 1983-1984

Docent, biofysik, KI, 1987

Professor, KI, 1998

Academic honours, awards and prizes

The Lindbom Award of the Royal Swedish Academy of Sciences, 1998

Publications

A subset of functional adaptation mutations alter propensity for α-helical conformation in the intrinsically disordered glucocorticoid receptor tau1core activation domain
Salamanova E, Costeira-paulo J, Han Kh, Kim Dh, Nilsson L, Wright Aph
Biochimica et biophysica acta 2018;1862(6):1452-1461

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
Hartono Yd, Ito M, Villa A, Nilsson L
The journal of physical chemistry. B 2018;122(3):1152-1160

Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids
Hartono Yd, Xu Y, Karshikoff A, Nilsson L, Villa A
Journal of chemical information and modeling 2018;58(4):773-783

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima
Morgunova E, Yin Y, Das Pk, Jolma A, Zhu F, Popov A, et al
eLife 2018;7():-

LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures
Pabon-martinez Yv, Xu Y, Villa A, Lundin Ke, Geny S, Nguyen Ch, et al
Scientific reports 2017;7(1):11043-

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid
Xu Y, Villa A, Nilsson L
Journal of computational chemistry 2017;38(15):1147-1157

Additive CHARMM force field for naturally occurring modified ribonucleotides
Xu Y, Vanommeslaeghe K, Aleksandrov A, Mackerell Ad, Nilsson L
Journal of computational chemistry 2016;37(10):896-912

Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus
Juneja A, Nilsson L, Villa A
Biophysical chemistry 2016;218():7-13

Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE
Van Bergen La, Alonso M, Palló A, Nilsson L, De Proft F, Messens J
Scientific reports 2016;6():30369-

Structural effects of modified ribonucleotides and magnesium in transfer RNAs
Xu Y, Mackerell Ad, Nilsson L
Bioorganic & medicinal chemistry 2016;24(20):4826-4834

Editorial preface
Nilsson L, Åqvist J
Biochimica et biophysica acta 2015;1850(5):859-860

Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules
Nilsson L
Biophysical journal 2015;108(12):2755-6

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations
Allnér O, Foloppe N, Nilsson L
The journal of physical chemistry. B 2015;119(3):1114-28

Rigidity versus flexibility: the dilemma of understanding protein thermal stability
Karshikoff A, Nilsson L, Ladenstein R
The FEBS journal 2015;282(20):3899-917

Structural insights into the DNA-binding specificity of E2F family transcription factors
Morgunova E, Yin Y, Jolma A, Dave K, Schmierer B, Popov A, et al
Nature communications 2015;6():10050-

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields
Deb I, Sarzynska J, Nilsson L, Lahiri A
JOURNAL OF CHEMICAL INFORMATION AND MODELING 2014;54(4):1129-42

Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics
Juneja A, Villa A, Nilsson L
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2014;10(8):3532-40

Rapid Communication Capturing the Destabilizing Effect of Dihydrouridine Through Molecular Simulations
Deb I, Sarzynska J, Nilsson L, Lahiri A
BIOPOLYMERS 2014;101(10):985-91

Synthesis and evaluation of antineurotoxicity properties of an amyloid-β peptide targeting ligand containing a triamino acid
Honcharenko D, Bose Pp, Maity J, Kurudenkandy Fr, Juneja A, Flöistrup E, et al
Organic & biomolecular chemistry 2014;12(34):6684-93

Triple helical DNA in a duplex context and base pair opening
Esguerra M, Nilsson L, Villa A
Nucleic acids research 2014;42(18):11329-38

Implicit Solvent Models and Stabilizing Effects of Mutations and Ligands on the Unfolding of the Amyloid beta-Peptide Central Helix
Juneja A, Ito M, Nilsson L
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2013;9(1):834-46

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study
Allnér O, Nilsson L, Villa A
RNA (New York, N.Y.) 2013;19(7):916-26

Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity
Nilsson L
Biophysical journal 2013;104(9):1840-1

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
Karshikoff A, Nilsson L, Foloppe N
BIOCHEMISTRY 2013;52(34):5730-45

Computational studies of LXR molecular interactions reveal an allosteric communication pathway
Burendahl S, Nilsson L
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2012;80(1):294-306

Effects of Ligands on Unfolding of the Amyloid beta-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations
Ito M, Johansson J, Stromberg R, Nilsson L
PLOS ONE 2012;7(1):e30510-

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations
Allner O, Nilsson L, Villa A
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2012;8(4):1493-502

Mycoredoxin-1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria
Van Laer K, Buts L, Foloppe N, Vertommen D, Van Belle K, Wahni K, et al
MOLECULAR MICROBIOLOGY 2012;86(4):787-804

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
Hart K, Foloppe N, Baker Cm, Denning Ej, Nilsson L, Mackerell Ad
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2012;8(1):348-362

The -Cys-X1-X2-Cys- Motif of Reduced Glutaredoxins Adopts a Consensus Structure That Explains the Low pK(a) of Its Catalytic Cysteine
Foloppe N, Vlamis-gardikas A, Nilsson L
BIOCHEMISTRY 2012;51(41):8189-207

Crystal Structure of the HIV-2 Neutralizing Fab Fragment 7C8 with High Specificity to the V3 Region of gp125
Uchtenhagen H, Friemann R, Raszewski G, Spetz Al, Nilsson L, Achour A
PLOS ONE 2011;6(4):e18767-

Impact of 2 '-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA
Denning Ej, Priyakumar Ud, Nilsson L, Mackerell Ad
JOURNAL OF COMPUTATIONAL CHEMISTRY 2011;32(9):1929-43

Multiple pH Regime Molecular Dynamics Simulation for pK Calculations
Nilsson L, Karshikoff A
PLOS ONE 2011;6(5):e20116-

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome
Allner O, Nilsson L
RNA-A PUBLICATION OF THE RNA SOCIETY 2011;17(12):2177-88

The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases
Uyar A, Kurkcuoglu O, Nilsson L, Doruker P
PHYSICAL BIOLOGY 2011;8(5):056001-

Unfolding of the Amyloid beta-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations
Ito M, Johansson J, Stromberg R, Nilsson L
PLOS ONE 2011;6(3):e17587-

Fatty Acids Derived from Royal Jelly Are Modulators of Estrogen Receptor Functions
Moutsatsou P, Papoutsi Z, Kassi E, Heldring N, Zhao Cy, Tsiapara A, et al
PLOS ONE 2010;5(12):e15594-

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
Juneja A, Numata J, Nilsson L, Knapp Ew
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2010;6(6):1871-83

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
Siponen Mi, Wisniewska M, Lehtio L, Johansson I, Svensson L, Raszewski G, et al
JOURNAL OF BIOLOGICAL CHEMISTRY 2010;285(34):25875-9

Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase
Talukdar A, Morgunova E, Duan Jx, Meining W, Foloppe N, Nilsson L, et al
BIOORGANIC & MEDICINAL CHEMISTRY 2010;18(10):3518-34

CHARMM: The Biomolecular Simulation Program
Brooks Br, Brooks Cl, Mackerell Ad, Nilsson L, Petrella Rj, Roux B, et al
JOURNAL OF COMPUTATIONAL CHEMISTRY 2009;30(10):1545-614

Does the Dynamic Stokes Shift Report on Slow Protein Hydration Dynamics?
Halle B, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY B 2009;113(24):8210-3

Efficient Table Lookup Without Inverse Square Roots for Calculation of Pair Wise Atomic Interactions in Classical Simulations
Nilsson L
JOURNAL OF COMPUTATIONAL CHEMISTRY 2009;30(9):1490-8

How Thioredoxin Dissociates Its Mixed Disulfide
Roos G, Foloppe N, Van Laer K, Wyns L, Nilsson L, Geerlings P, et al
PLOS COMPUTATIONAL BIOLOGY 2009;5(8):e1000461-

Ligand unbinding from the estrogen receptor: A computational study of pathways and ligand specificity
Burendahl S, Danciulescu C, Nilsson L
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2009;77(4):842-56

Structure-function defects of the twinkle amino-terminal region in progressive external ophthalmoplegia
Holmlund T, Farge G, Pande V, Korhonen J, Nilsson L, Falkenberg M
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE 2009;1792(2):132-9

Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes
Macchion Bn, Stromberg R, Nilsson L
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 2008;26(2):163-73

Cytosine ribose flexibility in DNA: a combined NMR C-13 spin relaxation and molecular dynamics simulation study
Duchardt E, Nilsson L, Schleucher J
NUCLEIC ACIDS RESEARCH 2008;36(12):4211-9

Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations
Pande V, Nilsson L
NUCLEIC ACIDS RESEARCH 2008;36(5):1508-16

Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study
Hart K, Nilsson L
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2008;73(2):325-37

Molecular dynamics simulations of human LRH-1: The impact of ligand binding in a constitutively active nuclear receptor
Burendahl S, Treuter E, Nilsson L
BIOCHEMISTRY 2008;47(18):5205-15

Molecular dynamics simulations of nucleic acid-protein complexes
Mackerell Ad, Nilsson L
CURRENT OPINION IN STRUCTURAL BIOLOGY 2008;18(2):194-9

Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia
Korhonen Ja, Pande V, Holmlund T, Farge G, Pham Xh, Nilsson L, et al
JOURNAL OF MOLECULAR BIOLOGY 2008;377(3):691-705

A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide
Mark P, Nilsson L
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 2007;36(3):213-24

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations
Watanabe T, Inadomi Y, Fukuzawa K, Nakano T, Tanaka S, Nilsson L, et al
JOURNAL OF PHYSICAL CHEMISTRY B 2007;111(32):9621-7

Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima
Danciulescu C, Ladenstein R, Nilsson L
BIOCHEMISTRY 2007;46(29):8537-49

Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution
Lahiri A, Sarzynska J, Nilsson L, Kulinski T
THEORETICAL CHEMISTRY ACCOUNTS 2007;117(2):267-273

Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs
Nystrom B, Nilsson L
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 2007;24(6):525-36

Stabilization of the catalytic thiolate in a mammalian glutaredoxin: Structure, dynamics and electrostatics of reduced pig glutaredoxin and its mutants
Foloppe N, Nilsson L
JOURNAL OF MOLECULAR BIOLOGY 2007;372(3):798-816

The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43
Porat A, Lillig Ch, Johansson C, Fernandes Ap, Nilsson L, Holmgren A, et al
BIOCHEMISTRY 2007;46(11):3366-77

Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations
Doruker P, Nilsson L, Kurkcuoglu O
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 2006;24(1):1-16

Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain
Duan Jx, Nilsson L
BIOCHEMISTRY 2006;45(24):7483-92

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
Law Mj, Linde Me, Chambers Ej, Oubridge C, Katsamba Ps, Nilsson L, et al
NUCLEIC ACIDS RESEARCH 2006;34(1):275-85

Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics
Carlsson P, Burendahl S, Nilsson L
BIOPHYSICAL JOURNAL 2006;91(9):3151-61

Urea parametrization for molecular dynamics simulations
Caballero-herrera A, Nilsson L
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 2006;758(2-3):139-148

Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization
Caballero-herrera A, Nordstrand K, Berndt Kd, Nilsson L
BIOPHYSICAL JOURNAL 2005;89(2):842-57

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization
Carlsson P, Koehler Kf, Nilsson L
MOLECULAR ENDOCRINOLOGY 2005;19(8):1960-77

Intrinsic relative stabilities of the neutral tautomers of arginine side-chain models
Norberg J, Foloppe N, Nilsson L
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2005;1(5):986-93

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA
Hart K, Nystrom B, Ohman M, Nilsson L
RNA-A PUBLICATION OF THE RNA SOCIETY 2005;11(5):609-18

Molecular origin of time-dependent fluorescence shifts in proteins
Nilsson L, Halle B
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2005;102(39):13867-72

Thermal unfolding simulations of a multimeric protein - Transition state and unfolding pathways
Duan Jx, Nilsson L
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2005;59(2):170-82

Toward a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides
Foloppe N, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY B 2005;109(18):9119-31

A single residue exchange between two HLA-B27 alleles triggers increased peptide flexibility
Starikov Eb, Nilsson L, Hulsmeyer M
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 2004;33(7):651-5

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

Human hereditary glutathione synthetase deficiency: kinetic properties of mutant enzymes
Njalsson R, Carlsson K, Bhansali V, Luo Jl, Nilsson L, Ladenstein R, et al
BIOCHEMICAL JOURNAL 2004;:489-94

Structural and functional analysis of mutations at the human hypoxanthine phosphorlibosyl transferase (HPRT1) locus
Duan Jx, Nilsson L, Lambert B
HUMAN MUTATION 2004;23(6):599-611

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

Advances in biomolecular simulations: methodology and recent applications
Norberg J, Nilsson L
QUARTERLY REVIEWS OF BIOPHYSICS 2003;36(3):257-306

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations
Sarzynska J, Nilsson L, Kulinski T
BIOPHYSICAL JOURNAL 2003;85(6):3445-59

Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling
Carlsson P, Nilsson L
JOURNAL OF COMPUTATIONAL CHEMISTRY 2003;24(12):1383-9

Molecular dynamics simulations of the E1/E2 transmembrane domain of the semliki forest virus
Caballero-herrera A, Nilsson L
BIOPHYSICAL JOURNAL 2003;85(6):3646-58

A molecular dynamics study of tryptophan in water
Mark P, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY B 2002;106(36):9440-9445

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

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: A quantum mechanical study
Foloppe N, Hartmann B, Nilsson L, Mackerell Ad
BIOPHYSICAL JOURNAL 2002;82(3):1554-69

Molecular dynamics applied to nucleic acids
Norberg J, Nilsson L
ACCOUNTS OF CHEMICAL RESEARCH 2002;35(6):465-72

Structural basis of biotin-RNA aptamer binding: a theoretical study
Starikov Eb, Nilsson L
CHEMICAL PHYSICS LETTERS 2002;363(1-2):39-44

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
Mark P, Nilsson L
JOURNAL OF COMPUTATIONAL CHEMISTRY 2002;23(13):1211-9

The role of residue 50 and hydration water molecules in homeodomain DNA recognition
Duan Jx, Nilsson L
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 2002;31(4):306-16

Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics
Foloppe N, Nilsson L, Mackerell Ad
BIOPOLYMERS 2001;61(1):61-76

Characterization of two novel mutations in the glucocorticoid receptor gene in patients with primary cortisol resistance
Ruiz M, Lind U, Gafvels M, Eggertsen G, Carlstedt-duke J, Nilsson L, et al
CLINICAL ENDOCRINOLOGY 2001;55(3):363-71

Exploring the idea of self-guided dynamics
Lahiri A, Nilsson L, Laaksonen A
JOURNAL OF CHEMICAL PHYSICS 2001;114(14):5993-5999

MD simulations of homomorphous PNA, DNA, and RNA single strands: Characterization and comparison of conformations and dynamics
Sen S, Nilsson L
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2001;123(30):7414-22

Modeling zinc sulfhydryl bonds in zinc fingers
Bredenberg J, Nilsson L
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2001;83(3-4):230-244

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

Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
Mark P, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY A 2001;105(43):9954-9960

Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: Comparison with functionally related proteins
Foloppe N, Sagemark J, Nordstrand K, Berndt Kd, Nilsson L
JOURNAL OF MOLECULAR BIOLOGY 2001;310(2):449-70

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge
Sarzynska J, Kulinski T, Nilsson L
BIOPHYSICAL JOURNAL 2000;79(3):1213-27

Molecular dynamics of the anticodon domain of yeast tRNA(Phe): Codon-anticodon interaction
Lahiri A, Nilsson L
BIOPHYSICAL JOURNAL 2000;79(5):2276-89

Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis
Tomic S, Nilsson L, Wade Rc
JOURNAL OF MEDICINAL CHEMISTRY 2000;43(9):1780-92

On the truncation of long-range electrostatic interactions in DNA
Norberg J, Nilsson L
BIOPHYSICAL JOURNAL 2000;79(3):1537-53

Effect of G40R mutation on the binding of human SRY protein to DNA: A molecular dynamics view
Tang Y, Nilsson L
PROTEINS-STRUCTURE FUNCTION AND GENETICS 1999;35(1):101-13

Examining the characteristics of chaos in biomolecular dynamics: a random matrix approximation
Lahiri A, Nilsson L
CHEMICAL PHYSICS LETTERS 1999;311(6):459-466

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex
Sen S, Nilsson L
BIOPHYSICAL JOURNAL 1999;77(4):1801-10

Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution
Tang Y, Nilsson L
BIOPHYSICAL JOURNAL 1999;77(3):1284-305

Some practical aspects of free energy calculations from molecular dynamics simulation
Sen S, Nilsson L
JOURNAL OF COMPUTATIONAL CHEMISTRY 1999;20(8):877-885

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
Eriksson Mal, Nilsson L
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 1999;28(2):102-11

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 (vol 28, pg 102, 1999)
Eriksson Mal, Nilsson L
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 1999;28(4):356-356

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation
Sen S, Nilsson L
BIOPHYSICAL JOURNAL 1999;77(4):1782-800

Interaction of human SRY protein with DNA: A molecular dynamics study
Tang Y, Nilsson L
PROTEINS-STRUCTURE FUNCTION AND GENETICS 1998;31(4):417-33

Molecular dynamics of duplex systems involving PNA: Structural and dynamical consequences of the nucleic acid backbone
Sen S, Nilsson L
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1998;120(4):619-631

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

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

Properties of dianionic oxyphosphorane intermediates from hybrid QM/MM simulation: implications for ribozyme reactions
Lahiri A, Nilsson L
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 1997;:51-55

Structural analysis of an anti-estradiol antibody
Lamminmaki U, Villoutreix Bo, Jauria P, Saviranta P, Vihinen M, Nilsson L, et al
MOLECULAR IMMUNOLOGY 1997;34(16-17):1215-26

A 1.2 ns molecular dynamics simulation of the ribonuclease T-1-3'-guanosine monophosphate complex
Elofsson A, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY 1996;100(7):2480-2488

Aromatic interactions define the binding of the alphavirus spike to its nucleocapsid
Skoging U, Vihinen M, Nilsson L, Liljestrom P
STRUCTURE 1996;4(5):519-29

Conformational free energy landscape of ApApA from molecular dynamics simulations
Norberg J, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY 1996;100(7):2550-2554

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

Glass transition in DNA from molecular dynamics simulations
Norberg J, Nilsson L
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 1996;93(19):10173-6

Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides
Norberg J, Nilsson L
BIOPOLYMERS 1996;39(6):765-8

Internal mobility of the oligonucleotide duplexes d(TCGCG)(2) and d(CGCGCG)(2) in aqueous solution from molecular dynamics simulations
Norberg J, Nilsson L
JOURNAL OF BIOMOLECULAR NMR 1996;7(4):305-14

DNA-BASED MUTATION ANALYSIS OF BRUTONS TYROSINE KINASE GENE IN PATIENTS WITH X-LINKED AGAMMAGLOBULINEMIA
Vorechovsky I, Vihinen M, Desaintbasile G, Honsova S, Hammarstrom L, Muller S, et al
HUMAN MOLECULAR GENETICS 1995;4(1):51-8

MODULATION OF DNA-BINDING SPECIFICITY WITHIN THE NUCLEAR RECEPTOR FAMILY BY SUBSTITUTIONS AT A SINGLE AMINO-ACID POSITION
Zilliacus J, Wright Aph, Carlstedtduke J, Nilsson L, Gustafsson Ja
PROTEINS-STRUCTURE FUNCTION AND GENETICS 1995;21(1):57-67

MOLECULAR-DYNAMICS SIMULATIONS OF THE GLUCOCORTICOID RECEPTOR DNA-BINDING DOMAIN IN COMPLEX WITH DNA AND FREE IN SOLUTION
Eriksson Mal, Hard T, Nilsson L
BIOPHYSICAL JOURNAL 1995;68(2):402-26

NMR RELAXATION-TIMES, DYNAMICS, AND HYDRATION OF A NUCLEIC-ACID FRAGMENT FROM MOLECULAR-DYNAMICS SIMULATIONS
Norberg J, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY 1995;99(40):14876-14884

ON THE PH-DEPENDENCE OF AMIDE PROTON-EXCHANGE RATES IN PROTEINS
Eriksson Mal, Hard T, Nilsson L
BIOPHYSICAL JOURNAL 1995;69(2):329-39

Potential of mean force calculations of the stacking unstacking process in single-stranded deoxyribodinucleoside monophosphates
Norberg J, Nilsson L
BIOPHYSICAL JOURNAL 1995;69(6):2277-85

STACKING FREE-ENERGY PROFILES FOR ALL 16 NATURAL RIBODINUCLEOSIDE MONOPHOSPHATES IN AQUEOUS-SOLUTION
Norberg J, Nilsson L
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1995;117(44):10832-10840

STRUCTURAL BASIS FOR PLECKSTRIN HOMOLOGY DOMAIN MUTATIONS IN X-LINKED AGAMMAGLOBULINEMIA
Vihinen M, Zvelebil Mjjm, Zhu Ql, Brooimans Ra, Ochs Hd, Zegers Bjm, et al
BIOCHEMISTRY 1995;34(5):1475-81

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Norberg J, Nilsson L
JOURNAL OF PHYSICAL CHEMISTRY 1995;99(35):13056-13058

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