Lennart Nilsson

Publications
CV
Public outreach and news

Articles

Article: NATURE COMMUNICATIONS. 2024;15(1):1865
A druggable conformational switch in the c-MYC transactivation domain
Lama D; Vosselman T; Sahin C; Liano-Pons J; Cerrato CP; Nilsson L; Teilum K; Lane DP; Landreh M; Arsenian Henriksson M
Article: BIOCHIMICA ET BIOPHYSICA ACTA - GENERAL SUBJECTS. 2024;1868(2):130534
Biomolecular dynamics in the 21st century
Brooks III CL; MacKerell Jr AD; Post CB; Nilsson L
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2023;19(11):3346-3358
Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation
Tamez A; Nilsson L; Mihailescu M-R; Evanseck JDD
Article: STRUCTURE. 2022;30(5):733-742.e7
A "spindle and thread"mechanism unblocks p53 translation N-terminal disorder
Kaldmae M; Vosselman T; Zhong X; Lama D; Chen G; Saluri M; Kronqvist N; Siau JW; Ng AS; Ghadessy FJ; Sabatier P; Vojtesek B; Sarr M; Sahin C; Osterlund N; Ilag LL; Vaananen VA; Sedimbi S; Arsenian-Henriksson M; Zubarev RA; Nilsson L; Koeck PJB; Rising A; Abelein A; Fritz N; Johansson J; Lane DP; Landreh M
Article: ANALYTICAL CHEMISTRY. 2019;91(17):11129-11137
Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells
Krmpot AJ; Nikolic SN; Oasa S; Papadopoulos DK; Vitali M; Oura M; Mikuni S; Thyberg P; Tisa S; Kinjo M; Nilsson L; Terenius L; Rigler R; Vukojevic V
Article: ACS CHEMICAL NEUROSCIENCE. 2019;10(3):1462-1477
Amyloid-β Peptide Targeting Peptidomimetics for Prevention of Neurotoxicity
Honcharenko D; Juneja A; Roshan F; Maity J; Galan-Acosta L; Biverstal H; Hjorth E; Johansson J; Fisahn A; Nilsson L; Stromberg R
Article: ACS OMEGA. 2019;4(2):3029-3044
Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNA^Phe: Differing Views from Different Force Fields
Deb I; Sarzynska J; Nilsson L; Lahiri A
Article: METHODS IN MOLECULAR BIOLOGY. 2019;2036:113-126
Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy.
Nilsson L; Villa A
Article: PLOS ONE. 2019;14(2):e0211651
The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study
Xu Y; Gissberg O; Pabon-Martinez YV; Wengel J; Lundin KE; Smith CIE; Zain R; Nilsson L; Villa A
Article: BIOCHIMICA ET BIOPHYSICA ACTA - GENERAL SUBJECTS. 2018;1862(6):1452-1461
A subset of functional adaptation mutations alter propensity for α-helical conformation in the intrinsically disordered glucocorticoid receptor taulcore activation domain
Salamanova E; Costeira-Paulo J; Han K-H; Kim D-H; Nilsson L; Wright APH
Article: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2018;58(4):773-783
Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids
Hartono YD; Xu Y; Karshikoff A; Nilsson L; Villa A
Article: ELIFE. 2018;7:e32963
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; Xu Y; Nilsson L; Taipale J
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2018;122(3):1152-1160
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
Article: SCIENTIFIC REPORTS. 2017;7(1):11043
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 C-H; Pedersen EB; Jorgensen PT; Wengel J; Nilsson L; Smith CIE; Zain R
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2017;38(15):1147-1157
The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid
Xu Y; Villa A; Nilsson L
Article: ACS OMEGA. 2017;2(5):2165-2177
Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies
Hartono YD; Pabon-Martinez YV; Uyar A; Wengel J; Lundin KE; Zain R; Smith CIE; Nilsson L; Villa A
Article: BIOPHYSICAL CHEMISTRY. 2016;218:7-13
Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus
Juneja A; Nilsson L; Villa A
Article: BIOORGANIC AND MEDICINAL CHEMISTRY. 2016;24(20):4826-4834
Structural effects of modified ribonucleotides and magnesium in transfer RNAs
Xu Y; MacKerell ADJ; Nilsson L
Article: SCIENTIFIC REPORTS. 2016;6:30369
Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE
van Bergen LAH; Alonso M; Pallo A; Nilsson L; De Proft F; Messens J
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2016;37(10):896-912
Additive CHARMM Force Field for Naturally Occurring Modified Ribonucleotides
Xu Y; Vanommeslaeghe K; Aleksandrov A; MacKerell ADJ; Nilsson L
Article: NATURE COMMUNICATIONS. 2015;6:10050
Structural insights into the DNA-binding specificity of E2F family transcription factors
Morgunova E; Yin Y; Jolma A; Dave K; Schmierer B; Popov A; Eremina N; Nilsson L; Taipale J
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2015;119(3):1114-1128
Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations
Allner O; Foloppe N; Nilsson L
Article: NUCLEIC ACIDS RESEARCH (NAR). 2014;42(18):11329-11338
Triple helical DNA in a duplex context and base pair opening
Esguerra M; Nilsson L; Villa A
Article: BIOPOLYMERS. 2014;101(10):985-991
Rapid Communication Capturing the Destabilizing Effect of Dihydrouridine Through Molecular Simulations
Deb I; Sarzynska J; Nilsson L; Lahiri A
Article: ORGANIC AND BIOMOLECULAR CHEMISTRY. 2014;12(34):6684-6693
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; Floistrup E; Biverstal H; Johansson J; Nilsson L; Fisahn A; Stromberg R
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2014;10(8):3532-3540
Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics
Juneja A; Villa A; Nilsson L
Article: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2014;54(4):1129-1142
Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields
Deb I; Sarzynska J; Nilsson L; Lahiri A
Article: BIOCHEMISTRY. 2013;52(34):5730-5745
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
Article: RNA: A PUBLICATION OF THE RNA SOCIETY. 2013;19(7):916-926
Loop-loop interaction in an adenine-sensing riboswitch: A molecular dynamics study
Allner O; Nilsson L; Villa A
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2013;9(1):834-846
Implicit Solvent Models and Stabilizing Effects of Mutations and Ligands on the Unfolding of the Amyloid β-Peptide Central Helix
Juneja A; Ito M; Nilsson L
Article: MOLECULAR MICROBIOLOGY. 2012;86(4):787-804
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; Roos G; Nilsson L; Mateos LM; Rawat M; van Nuland NAJ; Messens J
Article: BIOCHEMISTRY. 2012;51(41):8189-8207
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
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2012;8(4):1493-1502
Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations.
Allnér O; Nilsson L; Villa A
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2012;8(1):348-362
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 ADJ
Article: PLOS ONE. 2012;7(1):e30510
Effects of Ligands on Unfolding of the Amyloid β-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations
Ito M; Johansson J; Stromberg R; Nilsson L
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 2012;80(1):294-306
Computational studies of LXR molecular interactions reveal an allosteric communication pathway
Burendahl S; Nilsson L
Article: RNA: A PUBLICATION OF THE RNA SOCIETY. 2011;17(12):2177-2188
Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome
Allner O; Nilsson L
Article: PHYSICAL BIOLOGY. 2011;8(5):056001
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
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2011;32(9):1929-1943
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 ADJ
Article: PLOS ONE. 2011;6(4):e18767
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 A-L; Nilsson L; Achour A
Article: PLOS ONE. 2011;6(3):e17587
Unfolding of the Amyloid β-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations
Ito M; Johansson J; Stromberg R; Nilsson L
Article: PLOS ONE. 2011;6(5):e20116
Multiple pH Regime Molecular Dynamics Simulation for pK Calculations
Nilsson L; Karshikoff A
Article: PLOS ONE. 2010;5(12):e15594
Fatty Acids Derived from Royal Jelly Are Modulators of Estrogen Receptor Functions
Moutsatsou P; Papoutsi Z; Kassi E; Heldring N; Zhao C; Tsiapara A; Melliou E; Chrousos GP; Chinou I; Karshikoff A; Nilsson L; Dahlman-Wright K
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2010;285(34):25875-25879
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; Nilsson L; Sigvardsson M; Berglund H
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2010;6(6):1871-1883
Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
Juneja A; Numata J; Nilsson L; Knapp EW
Article: BIOORGANIC AND MEDICINAL CHEMISTRY. 2010;18(10):3518-3534
Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase
Talukdar A; Morgunova E; Duan J; Meining W; Foloppe N; Nilsson L; Bacher A; Illarionov B; Fischer M; Ladenstein R; Cushman M
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 2009;77(4):842-856
Ligand unbinding from the estrogen receptor: A computational study of pathways and ligand specificity
Burendahl S; Danciulescu C; Nilsson L
Article: PLOS COMPUTATIONAL BIOLOGY. 2009;5(8):e1000461
How Thioredoxin Dissociates Its Mixed Disulfide
Roos G; Foloppe N; Van Laer K; Wyns L; Nilsson L; Geerlings P; Messens J
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2009;30(9):1490-1498
Efficient Table Lookup Without Inverse Square Roots for Calculation of Pair Wise Atomic Interactions in Classical Simulations
Nilsson L
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2009;113(24):8210-8213
Does the Dynamic Stokes Shift Report on Slow Protein Hydration Dynamics?
Halle B; Nilsson L
Article: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2009;1792(2):132-139
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
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 2008;73(2):325-337
Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study
Hart K; Nilsson L
Article: JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS. 2008;26(2):163-173
Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes
Macchion BN; Stromberg R; Nilsson L
Article: NUCLEIC ACIDS RESEARCH (NAR). 2008;36(12):4211-4219
Cytosine ribose flexibility in DNA:: a combined NMR ¹³C spin relaxation and molecular dynamics simulation study
Duchardt E; Nilsson L; Schleucher J
Article: BIOCHEMISTRY. 2008;47(18):5205-5215
Molecular dynamics simulations of human LRH-1: The impact of ligand binding in a constitutively active nuclear receptor
Burendahl S; Treuter E; Nilsson L
Article: JOURNAL OF MOLECULAR BIOLOGY. 2008;377(3):691-705
Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia
Korhonen JA; Pande V; Holmlund T; Farge G; Pham XH; Nilsson L; Falkenberg M
Article: NUCLEIC ACIDS RESEARCH (NAR). 2008;36(5):1508-1516
Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations
Pande V; Nilsson L
Article: JOURNAL OF MOLECULAR BIOLOGY. 2007;372(3):798-816
Stabilization of the catalytic thiolate in a mammalian glutaredoxin: Structure, dynamics and electrostatics of reduced pig glutaredoxin and its mutants
Foloppe N; Nilsson L
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2007;111(32):9621-9627
DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations
Watanabe T; Inadomi Y; Fukuzawa K; Nakano T; Tanaka S; Nilsson L; Nagashima U
Article: BIOCHEMISTRY. 2007;46(29):8537-8549
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
Article: JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS. 2007;24(6):525-535
Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs
Nystrom B; Nilsson L
Article: BIOCHEMISTRY. 2007;46(11):3366-3377
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; Beckwith J
Article: EUROPEAN BIOPHYSICS JOURNAL. 2007;36(3):213-224
A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide
Mark P; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2006;91(9):3151-3161
Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics
Carlsson P; Burendahl S; Nilsson L
Article: JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS. 2006;24(1):1-15
Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations
Doruker P; Nilsson L; Kurkcuoglu O
Article: BIOCHEMISTRY. 2006;45(24):7483-7492
Effect of Zn²⁺ on DNA recognition and stability of the p53 DNA-binding domain
Duan J; Nilsson L
Article: NUCLEIC ACIDS RESEARCH (NAR). 2006;34(1):275-285
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; Haworth IS; Laird-Offringa IA
Article: COMPUTATIONAL AND THEORETICAL CHEMISTRY. 2006;758(2-3):139-148
Urea parametrization for molecular dynamics simulations
Caballero-Herrera A; Nilsson L
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2005;102(39):13867-13872
Molecular origin of time-dependent fluorescence shifts in proteins
Nilsson L; Halle B
Article: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2005;1(5):986-993
Intrinsic relative stabilities of the neutral tautomers of arginine side-chain models
Norberg J; Foloppe N; Nilsson L
Article: MOLECULAR ENDOCRINOLOGY. 2005;19(8):1960-1977
Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization
Carlsson P; Koehler KF; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2005;89(2):842-857
Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization
Caballero-Herrera A; Nordstrand K; Berndt KD; Nilsson L
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2005;109(18):9119-9131
Toward a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides
Foloppe N; Nilsson L
Article: RNA: A PUBLICATION OF THE RNA SOCIETY. 2005;11(5):609-618
Molecular dynamics simulations and free energy calculations of base flipping in dsRNA
Hart K; Nyström B; Öhman M; Nilsson L
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 2005;59(2):170-182
Thermal unfolding simulations of a multimeric protein - Transition state and unfolding pathways
Duan JX; Nilsson L
Article: EUROPEAN BIOPHYSICS JOURNAL. 2004;33(7):651-655
A single residue exchange between two HLA-B27 alleles triggers increased peptide flexibility
Starikov EB; Nilsson L; Hülsmeyer M
Article: BIOCHEMICAL JOURNAL. 2004;381(Pt 2):489-494
Human hereditary glutathione synthetase deficiency:: kinetic properties of mutant enzymes
Njålsson R; Carlsson K; Bhansali V; Luo JL; Nilsson L; Ladenstein R; Anderson M; Larsson A; Norgren S
Article: HUMAN MUTATION. 2004;23(6):599-611
Structural and functional analysis of mutations at the human hypoxanthine phosphorlibosyl transferase (HPRT1) locus
Duan JX; Nilsson L; Lambert B
Article: STRUCTURE. 2004;12(2):289-300
The glutaredoxin -C-P-Y-C- motif: Influence of peripheral residues
Foloppe N; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2003;85(6):3646-3658
Molecular dynamics simulations of the E1/E2 transmembrane domain of the semliki forest virus
Caballero-Herrera A; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2003;85(6):3445-3459
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations
Sarzynska J; Nilsson L; Kulinski T
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2003;24(12):1383-1389
Improved precision and efficiency of free energy calculations for small systems using λ-scaled atomic masses and separating conformational and transformational sampling
Carlsson P; Nilsson L
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2002;23(13):1211-1219
Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
Mark P; Nilsson L
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 2002;49(1):24-36
Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations
Bredenberg J; Nilsson L
Article: CHEMICAL PHYSICS LETTERS. 2002;363(1-2):39-44
Structural basis of biotin-RNA aptamer binding: a theoretical study
Starikov EB; Nilsson L
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2002;106(36):9440-9445
A molecular dynamics study of tryptophan in water
Mark P; Nilsson L
Article: EUROPEAN BIOPHYSICS JOURNAL. 2002;31(4):306-316
The role of residue 50 and hydration water molecules in homeodomain DNA recognition
Duan JX; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2002;82(3):1554-1569
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: A quantum mechanical study
Foloppe N; Hartmann B; Nilsson L; MacKerell AD
Article: JOURNAL OF PHYSICAL CHEMISTRY A. 2001;105(43):9954-9960
Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
Mark P; Nilsson L
Article: CLINICAL ENDOCRINOLOGY. 2001;55(3):363-371
Characterization of two novel mutations in the glucocorticoid receptor gene in patients with primary cortisol resistance
Ruiz M; Lind U; Gåfvels M; Eggertsen G; Carlstedt-Duke J; Nilsson L; Holtmann M; Stierna P; Wikström AC; Werner S
Article: JOURNAL OF PHYSICAL CHEMISTRY B. 2001;105(33):8028-8035
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
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2001;123(30):7414-7422
MD simulations of homomorphous PNA, DNA, and RNA single strands: Characterization and comparison of conformations and dynamics
Sen S; Nilsson L
Article: JOURNAL OF MOLECULAR BIOLOGY. 2001;310(2):449-470
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
Article: JOURNAL OF CHEMICAL PHYSICS. 2001;114(14):5993-5999
Exploring the idea of self-guided dynamics
Lahiri A; Nilsson L; Laaksonen A
Article: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY. 2001;83(3-4):230-244
Modeling zinc sulfhydryl bonds in zinc fingers
Bredenberg J; Nilsson L
Article: BIOPOLYMERS. 2001;61(1):61-76
Ab initio conformational analysis of nucleic acid components:: Intrinsic energetic contributions to nucleic acid structure and dynamics
Foloppe N; Nilsson L; MacKerell AD
Article: BIOPHYSICAL JOURNAL. 2000;79(5):2276-2289
Molecular dynamics of the anticodon domain of yeast tRNA^Phe:: Codon-anticodon interaction
Lahiri A; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2000;79(3):1537-1553
On the truncation of long-range electrostatic interactions in DNA
Norberg J; Nilsson L
Article: BIOPHYSICAL JOURNAL. 2000;79(3):1213-1227
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge
Sarzynska J; Kulinski T; Nilsson L
Article: JOURNAL OF MEDICINAL CHEMISTRY. 2000;43(9):1780-1792
Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis
Tomic S; Nilsson L; Wade RC
Article: CHEMICAL PHYSICS LETTERS. 1999;311(6):459-466
Examining the characteristics of chaos in biomolecular dynamics: a random matrix approximation
Lahiri A; Nilsson L
Article: BIOPHYSICAL JOURNAL. 1999;77(4):1801-1810
Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex
Sen S; Nilsson L
Article: BIOPHYSICAL JOURNAL. 1999;77(4):1782-1800
Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation
Sen S; Nilsson L
Article: BIOPHYSICAL JOURNAL. 1999;77(3):1284-1305
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
Article: JOURNAL OF COMPUTATIONAL CHEMISTRY. 1999;20(8):877-885
Some practical aspects of free energy calculations from molecular dynamics simulation
Sen S; Nilsson L
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 1999;35(1):101-113
Effect of G40R mutation on the binding of human SRY protein to DNA: A molecular dynamics view
Tang Y; Nilsson L
Article: EUROPEAN BIOPHYSICS JOURNAL. 1999;28(2):102-111
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
Article: PROTEIN ENGINEERING, DESIGN AND SELECTION. 1998;11(7):589-600
Structural and dynamic effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain
Eriksson MAL; Nilsson L
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 1998;31(4):417-433
Interaction of human SRY protein with DNA: A molecular dynamics study
Tang Y; Nilsson L
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 1998;120(4):619-631
Molecular dynamics of duplex systems involving PNA: Structural and dynamical consequences of the nucleic acid backbone
Sen S; Nilsson L
Article: BIOPHYSICAL JOURNAL. 1998;74(1):394-402
Solvent influence on base stacking
Norberg J; Nilsson L
Article: MOLECULAR IMMUNOLOGY. 1997;34(16-17):1215-1226
Structural analysis of an anti-estradiol antibody
Lamminmäki U; Villoutreix BO; Jauria P; Saviranta P; Vihinen M; Nilsson L; Teleman O; Lövgren T
Article: BIOPOLYMERS. 1996;39(6):765-768
Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides
Norberg J; Nilsson L
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 1996;93(19):10173-10176
Glass transition in DNA from molecular dynamics simulations
Norberg J; Nilsson L
Article: JOURNAL OF BIOMOLECULAR NMR. 1996;7(4):305-314
Internal mobility of the oligonucleotide duplexes d(TCGCG)(2) and d(CGCGCG)(2) in aqueous solution from molecular dynamics simulations
Norberg J; Nilsson L
Article: STRUCTURE. 1996;4(5):519-529
Aromatic interactions define the binding of the alphavirus spike to its nucleocapsid
Skoging U; Vihinen M; Nilsson L; Liljestrom P
Article: JOURNAL OF CHEMICAL PHYSICS. 1996;104(15):6052-6057
Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)(2) and r(GCGCGCGCGCGC)(2)
Norberg J; Nilsson L
Article: JOURNAL OF PHYSICAL CHEMISTRY. 1996;100(7):2480-2488
A 1.2 ns molecular dynamics simulation of the ribonuclease T-1-3'-guanosine monophosphate complex
Elofsson A; Nilsson L
Article: JOURNAL OF PHYSICAL CHEMISTRY. 1996;100(7):2550-2554
Conformational free energy landscape of ApApA from molecular dynamics simulations
Norberg J; Nilsson L
Article: BIOPHYSICAL JOURNAL. 1995;69(6):2277-2285
Potential of mean force calculations of the stacking unstacking process in single-stranded deoxyribodinucleoside monophosphates
Norberg J; Nilsson L
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 1995;117(44):10832-10840
STACKING FREE-ENERGY PROFILES FOR ALL 16 NATURAL RIBODINUCLEOSIDE MONOPHOSPHATES IN AQUEOUS-SOLUTION
NORBERG J; NILSSON L
Article: JOURNAL OF MOLECULAR BIOLOGY. 1995;253(3):453-472
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
ERIKSSON MAL; NILSSON L
Article: JOURNAL OF PHYSICAL CHEMISTRY. 1995;99(40):14876-14884
NMR RELAXATION-TIMES, DYNAMICS, AND HYDRATION OF A NUCLEIC-ACID FRAGMENT FROM MOLECULAR-DYNAMICS SIMULATIONS
NORBERG J; NILSSON L
Article: JOURNAL OF PHYSICAL CHEMISTRY. 1995;99(35):13056-13058
TEMPERATURE-DEPENDENCE OF THE STACKING PROPENSITY OF ADENYLYL-3',5'-ADENOSINE
NORBERG J; NILSSON L
Article: BIOPHYSICAL JOURNAL. 1995;69(2):329-339
ON THE PH-DEPENDENCE OF AMIDE PROTON-EXCHANGE RATES IN PROTEINS
ERIKSSON MAL; HARD T; NILSSON L
Article: BIOCHEMISTRY. 1995;34(5):1475-1481
STRUCTURAL BASIS FOR PLECKSTRIN HOMOLOGY DOMAIN MUTATIONS IN X-LINKED AGAMMAGLOBULINEMIA
VIHINEN M; ZVELEBIL M; ZHU QL; BROOIMANS RA; OCHS HD; ZEGERS BJM; NILSSON L; WATERFIELD MD; SMITH CIE
Article: BIOPHYSICAL JOURNAL. 1995;68(2):402-426
MOLECULAR-DYNAMICS SIMULATIONS OF THE GLUCOCORTICOID RECEPTOR DNA-BINDING DOMAIN IN COMPLEX WITH DNA AND FREE IN SOLUTION
ERIKSSON MAL; HARD T; NILSSON L
Article: HUMAN MOLECULAR GENETICS. 1995;4(1):51-58
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; NILSSON L; FISCHER A; SMITH CIE
Article: PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS. 1995;21(1):57-67
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
Show more

All other publications

Review: THE FEBS JOURNAL. 2015;282(20):3899-3917
Rigidity versus flexibility: the dilemma of understanding protein thermal stability
Karshikoff A; Nilsson L; Ladenstein R
Other: BIOPHYSICAL JOURNAL. 2015;108(12):2755-2756
Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules
Nilsson L
Editorial comment: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2015;1850(5):859-860
Editorial preface.
Nilsson L; Åqvist J
Other: BIOPHYSICAL JOURNAL. 2013;104(9):1840-1841
Sophisticated Modeling Uncovers Atomic DNA Structure in Bacteriophage Φ29 Cavity
Nilsson L
Review: JOURNAL OF COMPUTATIONAL CHEMISTRY. 2009;30(10):1545-1614
CHARMM: The Biomolecular Simulation Program
Brooks BR; Brooks CLIII; Mackerell ADJ; Nilsson L; Petrella RJ; Roux B; Won Y; Archontis G; Bartels C; Boresch S; Caflisch A; Caves L; Cui Q; Dinner AR; Feig M; Fischer S; Gao J; Hodoscek M; Im W; Kuczera K; Lazaridis T; Ma J; Ovchinnikov V; Paci E; Pastor RW; Post CB; Pu JZ; Schaefer M; Tidor B; Venable RM; Woodcock HL; Wu X; Yang W; York DM; Karplus M
Review: CURRENT OPINION IN STRUCTURAL BIOLOGY. 2008;18(2):194-199
Molecular dynamics simulations of nucleic acid-protein complexes
MacKerell ADJ; Nilsson L
Published conference paper: THEORETICAL CHEMISTRY ACCOUNTS. 2007;117(2):267-273
Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution
Lahiri A; Sarzynska J; Nilsson L; Kulinski T
Editorial comment: CHEMICAL PHYSICS LETTERS. 2004;393(1-3):282-283
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
Review: QUARTERLY REVIEWS OF BIOPHYSICS. 2003;36(3):257-306
Advances in biomolecular simulations: methodology and recent applications
Norberg J; Nilsson L
Review: ACCOUNTS OF CHEMICAL RESEARCH. 2002;35(6):465-472
Molecular dynamics applied to nucleic acids
Norberg J; Nilsson L
Corrigendum: EUROPEAN BIOPHYSICS JOURNAL. 1999;28(4):356
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
Published conference paper: COMPUTATIONAL AND THEORETICAL CHEMISTRY. 1997;419:51-55
Properties of dianionic oxyphosphorane intermediates from hybrid QM/MM simulation: implications for ribozyme reactions
Lahiri A; Nilsson L

Employments

Professor Emeritus/Emerita, Department of Medicine, Huddinge, Karolinska Institutet, 2024-2025

Degrees and Education

Docent, Karolinska Institutet, 1987

Articles

All other publications

Employments

Degrees and Education

News from KI

Events from KI