Lennart Nilsson, Ph.D. - Publications

Affiliations: 
Biosciences and Nutrition Karolinska Institute, Stockholm, Sweden 
Area:
Computational chemistry, biophysics, nucleic acids, proteins
Website:
http://www.csb.ki.se/md/md.html

118 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Krmpot AJ, Nikolić 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. Functional Fluorescence Microscopy Imaging (fFMI). Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells. Analytical Chemistry. PMID 31364842 DOI: 10.1021/Acs.Analchem.9B01813  0.96
2019 Xu Y, Gissberg O, Pabon-Martinez YV, Wengel J, Lundin KE, Smith CIE, Zain R, Nilsson L, Villa A. The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study. Plos One. 14: e0211651. PMID 30753192 DOI: 10.1371/Journal.Pone.0211651  0.36
2018 Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J. Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima. Elife. 7. PMID 29638214 DOI: 10.7554/Elife.32963  0.36
2018 Hartono YD, Xu Y, Karshikoff A, Nilsson L, Villa A. Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids. Journal of Chemical Information and Modeling. PMID 29537270 DOI: 10.1021/Acs.Jcim.7B00741  0.36
2017 Pabon-Martinez YV, Xu Y, Villa A, Lundin KE, Geny S, Nguyen CH, Pedersen EB, Jørgensen PT, Wengel J, Nilsson L, Smith CIE, Zain R. LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures. Scientific Reports. 7: 11043. PMID 28887512 DOI: 10.1038/S41598-017-09147-8  0.36
2017 Xu Y, Villa A, Nilsson L. The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. Journal of Computational Chemistry. PMID 28101966 DOI: 10.1002/Jcc.24692  0.36
2016 Xu Y, MacKerell AD, Nilsson L. Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorganic & Medicinal Chemistry. PMID 27364608 DOI: 10.1016/J.Bmc.2016.06.037  0.96
2014 Deb I, Sarzynska J, Nilsson L, Lahiri A. Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations. Biopolymers. 101: 985-91. PMID 24729441 DOI: 10.1002/Bip.22495  0.96
2014 Deb I, Sarzynska J, Nilsson L, Lahiri A. Conformational preferences of modified uridines: comparison of AMBER derived force fields. Journal of Chemical Information and Modeling. 54: 1129-42. PMID 24697757 DOI: 10.1021/Ci400582A  0.96
2013 Karshikoff A, Nilsson L, Foloppe N. 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. Biochemistry. 52: 5730-45. PMID 23879632 DOI: 10.1021/Bi400500E  0.96
2013 Allnér O, Nilsson L, Villa A. Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. Rna (New York, N.Y.). 19: 916-26. PMID 23716711 DOI: 10.1261/Rna.037549.112  0.96
2013 Nilsson L. Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity. Biophysical Journal. 104: 1840-1. PMID 23663824 DOI: 10.1016/J.Bpj.2013.03.043  0.96
2013 Juneja A, Ito M, Nilsson L. Implicit solvent models and stabilizing effects of mutations and ligands on the unfolding of the amyloid β-peptide central helix Journal of Chemical Theory and Computation. 9: 834-846. DOI: 10.1021/ct300941v  0.96
2012 Allnér O, Nilsson L, Villa A. Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations. Journal of Chemical Theory and Computation. 8: 1493-502. PMID 26596759 DOI: 10.1021/Ct3000734  0.96
2012 Van Laer K, Buts L, Foloppe N, Vertommen D, Van Belle K, Wahni K, Roos G, Nilsson L, Mateos LM, Rawat M, van Nuland NA, Messens J. Mycoredoxin-1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria. Molecular Microbiology. 86: 787-804. PMID 22970802 DOI: 10.1111/Mmi.12030  0.96
2012 Foloppe N, Vlamis-Gardikas A, Nilsson L. The -Cys-X1-X2-Cys- motif of reduced glutaredoxins adopts a consensus structure that explains the low pK(a) of its catalytic cysteine. Biochemistry. 51: 8189-207. PMID 22966829 DOI: 10.1021/Bi3006576  0.96
2012 Hart K, Foloppe N, Baker CM, Denning EJ, Nilsson L, Mackerell AD. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. Journal of Chemical Theory and Computation. 8: 348-362. PMID 22368531 DOI: 10.1021/Ct200723Y  0.96
2012 Ito M, Johansson J, Strömberg R, Nilsson L. Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. Plos One. 7: e30510. PMID 22291970 DOI: 10.1371/Journal.Pone.0030510  0.96
2012 Burendahl S, Nilsson L. Computational studies of LXR molecular interactions reveal an allosteric communication pathway. Proteins. 80: 294-306. PMID 22072626 DOI: 10.1002/Prot.23209  0.96
2011 Allnér O, Nilsson L. Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. Rna (New York, N.Y.). 17: 2177-88. PMID 22028366 DOI: 10.1261/Rna.029231.111  0.96
2011 Uyar A, Kurkcuoglu O, Nilsson L, Doruker P. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Physical Biology. 8: 056001. PMID 21791727 DOI: 10.1088/1478-3975/8/5/056001  0.96
2011 Nilsson L, Karshikoff A. Multiple pH regime molecular dynamics simulation for pK calculations. Plos One. 6: e20116. PMID 21647418 DOI: 10.1371/Journal.Pone.0020116  0.96
2011 Uchtenhagen H, Friemann R, Raszewski G, Spetz AL, Nilsson L, Achour A. Crystal structure of the HIV-2 neutralizing Fab fragment 7C8 with high specificity to the V3 region of gp125. Plos One. 6: e18767. PMID 21541316 DOI: 10.1371/Journal.Pone.0018767  0.96
2011 Denning EJ, Priyakumar UD, Nilsson L, Mackerell AD. Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. Journal of Computational Chemistry. 32: 1929-43. PMID 21469161 DOI: 10.1002/Jcc.21777  0.96
2011 Ito M, Johansson J, Strömberg R, Nilsson L. Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. Plos One. 6: e17587. PMID 21408230 DOI: 10.1371/Journal.Pone.0017587  0.96
2010 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. Fatty acids derived from royal jelly are modulators of estrogen receptor functions. Plos One. 5: e15594. PMID 21203528 DOI: 10.1371/Journal.Pone.0015594  0.96
2010 Siponen MI, Wisniewska M, Lehtiö L, Johansson I, Svensson L, Raszewski G, Nilsson L, Sigvardsson M, Berglund H. 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. 285: 25875-9. PMID 20592035 DOI: 10.1074/Jbc.C110.150482  0.96
2010 Talukdar A, Morgunova E, Duan J, Meining W, Foloppe N, Nilsson L, Bacher A, Illarionov B, Fischer M, Ladenstein R, Cushman M. Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase. Bioorganic & Medicinal Chemistry. 18: 3518-34. PMID 20430628 DOI: 10.1016/J.Bmc.2010.03.072  0.96
2010 Juneja A, Numata J, Nilsson L, Knapp EW. Merging implicit with explicit solvent simulations: Polyethylene glycol Journal of Chemical Theory and Computation. 6: 1871-1883. DOI: 10.1021/ct100075m  0.96
2009 Roos G, Foloppe N, Van Laer K, Wyns L, Nilsson L, Geerlings P, Messens J. How thioredoxin dissociates its mixed disulfide. Plos Computational Biology. 5: e1000461. PMID 19675666 DOI: 10.1371/Journal.Pcbi.1000461  0.96
2009 Burendahl S, Danciulescu C, Nilsson L. Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity. Proteins. 77: 842-56. PMID 19626711 DOI: 10.1002/Prot.22503  0.96
2009 Halle B, Nilsson L. Does the dynamic Stokes shift report on slow protein hydration dynamics? The Journal of Physical Chemistry. B. 113: 8210-3. PMID 19462949 DOI: 10.1021/Jp9027589  0.96
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  0.96
2009 Holmlund T, Farge G, Pande V, Korhonen J, Nilsson L, Falkenberg M. Structure-function defects of the twinkle amino-terminal region in progressive external ophthalmoplegia. Biochimica Et Biophysica Acta. 1792: 132-9. PMID 19084593 DOI: 10.1016/J.Bbadis.2008.11.009  0.96
2009 Nilsson L. Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations. Journal of Computational Chemistry. 30: 1490-8. PMID 19072764 DOI: 10.1002/Jcc.21169  0.96
2008 Macchion BN, Strömberg R, Nilsson L. Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes. Journal of Biomolecular Structure & Dynamics. 26: 163-73. PMID 18597538 DOI: 10.1080/07391102.2008.10507232  0.96
2008 Duchardt E, Nilsson L, Schleucher J. Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study. Nucleic Acids Research. 36: 4211-9. PMID 18579564 DOI: 10.1093/Nar/Gkn375  0.96
2008 Hart K, Nilsson L. Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study. Proteins. 73: 325-37. PMID 18433057 DOI: 10.1002/Prot.22062  0.96
2008 Burendahl S, Treuter E, Nilsson L. Molecular dynamics simulations of human LRH-1: the impact of ligand binding in a constitutively active nuclear receptor. Biochemistry. 47: 5205-15. PMID 18410128 DOI: 10.1021/Bi7025084  0.96
2008 Mackerell AD, Nilsson L. Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology. 18: 194-9. PMID 18281210 DOI: 10.1016/J.Sbi.2007.12.012  0.96
2008 Korhonen JA, Pande V, Holmlund T, Farge G, Pham XH, Nilsson L, Falkenberg M. Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia. Journal of Molecular Biology. 377: 691-705. PMID 18279890 DOI: 10.1016/J.Jmb.2008.01.035  0.96
2008 Pande V, Nilsson L. Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Research. 36: 1508-16. PMID 18203740 DOI: 10.1093/Nar/Gkm1182  0.96
2007 Foloppe N, Nilsson L. Stabilization of the catalytic thiolate in a mammalian glutaredoxin: structure, dynamics and electrostatics of reduced pig glutaredoxin and its mutants. Journal of Molecular Biology. 372: 798-816. PMID 17681533 DOI: 10.1016/J.Jmb.2007.05.101  0.96
2007 Watanabe T, Inadomi Y, Fukuzawa K, Nakano T, Tanaka S, Nilsson L, Nagashima U. DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations. The Journal of Physical Chemistry. B. 111: 9621-7. PMID 17649990 DOI: 10.1021/Jp071710V  0.96
2007 Danciulescu C, Ladenstein R, Nilsson L. Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima. Biochemistry. 46: 8537-49. PMID 17602502 DOI: 10.1021/Bi7004398  0.96
2007 Nyström B, Nilsson L. Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs. Journal of Biomolecular Structure & Dynamics. 24: 525-36. PMID 17508774 DOI: 10.1080/07391102.2007.10507141  0.96
2007 Porat A, Lillig CH, Johansson C, Fernandes AP, Nilsson L, Holmgren A, Beckwith J. The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43. Biochemistry. 46: 3366-77. PMID 17305371 DOI: 10.1021/Bi6024353  0.96
2007 Mark P, Nilsson L. A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide European Biophysics Journal. 36: 213-224. PMID 17225137 DOI: 10.1007/S00249-006-0121-3  0.96
2007 Lahiri A, Sarzynska J, Nilsson L, Kulinski T. Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution Theoretical Chemistry Accounts. 117: 267-273. DOI: 10.1007/S00214-006-0141-1  0.96
2007 Tu Y, Nilsson L, Laaksonen A. A highly efficient ab initio tight-binding-like approximate density-functional quantum mechanical method Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4699: 100-108.  0.96
2006 Carlsson P, Burendahl S, Nilsson L. Unbinding of Retinoic Acid from the Retinoic Acid Receptor by Random Expulsion Molecular Dynamics Biophysical Journal. 91: 3151-3161. PMID 16891362 DOI: 10.1529/Biophysj.106.082917  0.96
2006 Doruker P, Nilsson L, Kurkcuoglu O. Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations Journal of Biomolecular Structure and Dynamics. 24: 1-15. PMID 16780370 DOI: 10.1080/07391102.2006.10507093  0.96
2006 Duan J, Nilsson L. Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain Biochemistry. 45: 7483-7492. PMID 16768444 DOI: 10.1021/Bi0603165  0.96
2006 Law MJ, Linde ME, Chambers EJ, Oubridge C, Katsamba PS, Nilsson L, Haworth IS, Laird-Offringa IA. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Research. 34: 275-85. PMID 16407334 DOI: 10.1093/Nar/Gkj436  0.96
2006 Caballero-Herrera A, Nilsson L. Urea parametrization for molecular dynamics simulations Journal of Molecular Structure: Theochem. 758: 139-148. DOI: 10.1016/J.Theochem.2005.10.018  0.96
2006 Goto H, Obata S, Kamakura T, Nakayama N, Sato M, Nakajima Y, Nagashima U, Watanabe T, Inadomi Y, Ito M, Nishikawa T, Nakano T, Nilsson L, Tanaka S, Fukuzawa K, et al. Drug discovery using grid technology Modern Methods For Theoretical Physical Chemistry of Biopolymers. 227-248. DOI: 10.1016/B978-044452220-7/50076-9  0.96
2006 Elliott J, Starikov EB, Crawshaw J, Claiden P, Nilsson L, Windle A. Nucleation of polyglutamine amyloid fibres modelling using molecular dynamics Modern Methods For Theoretical Physical Chemistry of Biopolymers. 211-226. DOI: 10.1016/B978-044452220-7/50075-7  0.96
2006 Bredenberg J, Mark P, Nilsson L. Solvent effects on biomolecular dynamics simulations. A comparison between TIP3P, SPC and SPC/E water models acting on the Glucocorticoid receptor DNA-binding domain Modern Methods For Theoretical Physical Chemistry of Biopolymers. 123-135. DOI: 10.1016/B978-044452220-7/50070-8  0.96
2006 MacKerell AD, Nilsson L. Theoretical studies of nucleic acids and nucleic acid-protein complexes using charmm Computational Studies of Rna and Dna. 73-94. DOI: 10.1007/978-1-4020-4851-3_3  0.96
2005 Foloppe N, Nilsson L. Toward a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides Journal of Physical Chemistry B. 109: 9119-9131. PMID 16852085 DOI: 10.1021/Jp044513U  0.96
2005 Nilsson L, Halle B. Molecular origin of time-dependent fluorescence shifts in proteins Proceedings of the National Academy of Sciences of the United States of America. 102: 13867-13872. PMID 16162674 DOI: 10.1073/Pnas.0504181102  0.96
2005 Caballero-Herrera A, Nordstrand K, Berndt KD, Nilsson L. Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization Biophysical Journal. 89: 842-857. PMID 15908578 DOI: 10.1529/Biophysj.105.061978  0.96
2005 Hart K, Nyström B, Öhman M, Nilsson L. Molecular dynamics simulations and free energy calculations of base flipping in dsRNA Rna. 11: 609-618. PMID 15811914 DOI: 10.1261/Rna.7147805  0.96
2005 Carlsson P, Koehler KF, Nilsson L. Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization Molecular Endocrinology. 19: 1960-1977. PMID 15774500 DOI: 10.1210/Me.2004-0203  0.96
2005 Duan J, Nilsson L. Thermal unfolding simulations of a multimeric protein - Transition state and unfolding pathways Proteins: Structure, Function and Genetics. 59: 170-182. PMID 15723359 DOI: 10.1002/Prot.20407  0.96
2005 Norberg J, Foloppe N, Nilsson L. Intrinsic relative stabilities of the neutral tautomers of arginine side-chain models Journal of Chemical Theory and Computation. 1: 986-993. DOI: 10.1021/Ct049849M  0.96
2004 Duan J, Nilsson L, Lambert B. Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus Human Mutation. 23: 599-611. PMID 15146465 DOI: 10.1002/Humu.20047  0.96
2004 Njålsson R, Carlsson K, Bhansali V, Luo JL, Nilsson L, Ladenstein R, Anderson M, Larsson A, Norgren S. Human hereditary glutathione synthetase deficiency: Kinetic properties of mutant enzymes Biochemical Journal. 381: 489-494. PMID 15056072 DOI: 10.1042/Bj20040114  0.96
2004 Starikow EB, Nilsson L, Hülsmeyer M. A single residue exchange between two HLA-B27 alleles triggers increased peptide flexibility European Biophysics Journal. 33: 651-655. PMID 15014909 DOI: 10.1007/S00249-004-0390-7  0.96
2004 Foloppe N, Nilsson L. The Glutaredoxin -C-P-Y-C- Motif: Influence of Peripheral Residues Structure. 12: 289-300. PMID 14962389 DOI: 10.1016/J.Str.2004.01.009  0.96
2004 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 Chemical Physics Letters. 393: 282-283. DOI: 10.1016/J.Cplett.2004.06.046  0.96
2003 Norberg J, Nilsson L. Advances in biomolecular simulations: Methodology and recent applications Quarterly Reviews of Biophysics. 36: 257-306. PMID 15029826 DOI: 10.1017/S0033583503003895  0.96
2003 Caballero-Herrera A, Nilsson L. Molecular Dynamics Simulations of the E1/E2 Transmembrane Domain of the Semliki Forest Virus Biophysical Journal. 85: 3646-3658. PMID 14645057 DOI: 10.1016/S0006-3495(03)74782-1  0.96
2003 Sarzynska J, Nilsson L, Kulinski T. Effects of Base Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy Simulations Biophysical Journal. 85: 3445-3459. PMID 14645041 DOI: 10.1016/S0006-3495(03)74766-3  0.96
2003 Carlsson P, Nilsson L. Improved precision and efficiency of free energy calculations for small systems using λ-scaled atomic masses and separating conformational and transformational sampling Journal of Computational Chemistry. 24: 1383-1389. DOI: 10.1002/Jcc.10221  0.96
2002 Bredenberg J, Nilsson L. Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations Proteins: Structure, Function and Genetics. 49: 24-36. PMID 12211013 DOI: 10.1002/Prot.10195  0.96
2002 Duan J, Nilsson L. The role of residue 50 and hydration water molecules in homeodomain DNA recognition European Biophysics Journal. 31: 306-316. PMID 12122477 DOI: 10.1007/S00249-002-0217-3  0.96
2002 Norberg J, Nilsson L. Molecular dynamics applied to nucleic acids Accounts of Chemical Research. 35: 465-472. PMID 12069632 DOI: 10.1021/Ar010026A  0.96
2002 Foloppe N, Hartmann B, Nilsson L, MacKerell AD. Intrinsic conformational energetics associated with the glycosyl torsion in DNA: A quantum mechanical study Biophysical Journal. 82: 1554-1569. PMID 11867468 DOI: 10.1016/S0006-3495(02)75507-0  0.96
2002 Mark P, Nilsson L. A molecular dynamics study of tryptophan in water Journal of Physical Chemistry B. 106: 9440-9445. DOI: 10.1021/Jp025965E  0.96
2002 Starikov EB, Nilsson L. Structural basis of biotin-RNA aptamer binding: A theoretical study Chemical Physics Letters. 363: 39-44. DOI: 10.1016/S0009-2614(02)01143-0  0.96
2002 Mark P, Nilsson L. Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations Journal of Computational Chemistry. 23: 1211-1219. DOI: 10.1002/Jcc.10117  0.96
2001 Foloppe N, Nilsson L, MacKerell AD. Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics Biopolymers. 61: 61-76. PMID 11891629 DOI: 10.1002/1097-0282(2001)61:1<61::Aid-Bip10047>3.0.Co;2-1  0.96
2001 Ruiz M, Lind U, Gåfvels M, Eggertsen G, Carlstedt-Duke J, Nilsson L, Holtmann M, Stierna P, Wikström AC, Werner S. Characterization of two novel mutations in the glucocorticoid receptor gene in patients with primary cortisol resistance Clinical Endocrinology. 55: 363-371. PMID 11589680 DOI: 10.1046/J.1365-2265.2001.01323.X  0.96
2001 Sen S, Nilsson L. MD simulations of homomorphous PNA, DNA, and RNA single strands: Characterization and comparison of conformations and dynamics Journal of the American Chemical Society. 123: 7414-7422. PMID 11472173 DOI: 10.1021/Ja0032632  0.96
2001 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 Journal of Molecular Biology. 310: 449-470. PMID 11428900 DOI: 10.1006/Jmbi.2001.4767  0.96
2001 Lahiri A, Nilsson L, Laaksonen A. Exploring the idea of self-guided dynamics Journal of Chemical Physics. 114: 5993-5999. DOI: 10.1063/1.1351854  0.96
2001 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 Journal of Physical Chemistry B. 105: 8028-8035. DOI: 10.1021/Jp0044781  0.96
2001 Mark P, Nilsson L. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K Journal of Physical Chemistry A. 105: 9954-9960. DOI: 10.1021/Jp003020W  0.96
2001 Bredenberg J, Nilsson L. Modeling zinc sulfhydryl bonds in zinc fingers International Journal of Quantum Chemistry. 83: 230-244. DOI: 10.1002/Qua.1214  0.96
2001 Klier J, Bredenberg J, Nilsson L. Think big: Entwicklungsumgebung für verteilte anwendungen Etz, Elektrotechnik Und Automation. 122: 84+86.  0.96
2000 Lahiri A, Nilsson L. Molecular dynamics of the anticodon domain of yeast tRNA(Phe): Codon-anticodon interaction Biophysical Journal. 79: 2276-2289. PMID 11053108 DOI: 10.1016/S0006-3495(00)76474-5  0.96
2000 Norberg J, Nilsson L. On the truncation of long-range electrostatic interactions in DNA Biophysical Journal. 79: 1537-1553. PMID 10969015 DOI: 10.1016/S0006-3495(00)76405-8  0.96
2000 Sarzynska J, Kulinski T, Nilsson L. Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge Biophysical Journal. 79: 1213-1227. PMID 10968986 DOI: 10.1016/S0006-3495(00)76376-4  0.96
2000 Tomic S, Nilsson L, Wade RC. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis Journal of Medicinal Chemistry. 43: 1780-1792. PMID 10794695 DOI: 10.1021/Jm9911175  0.96
1999 Sen S, Nilsson L. Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex Biophysical Journal. 77: 1801-1810. PMID 10512804 DOI: 10.1016/S0006-3495(99)77025-6  0.96
1999 Sen S, Nilsson L. Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation Biophysical Journal. 77: 1782-1800. PMID 10512803 DOI: 10.1016/S0006-3495(99)77024-4  0.96
1999 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 Biophysical Journal. 77: 1284-1305. PMID 10465742 DOI: 10.1016/S0006-3495(99)76979-1  0.96
1999 Lahiri A, Nilsson L. Examining the characteristics of chaos in biomolecular dynamics: A random matrix approximation Chemical Physics Letters. 311: 459-466. DOI: 10.1016/S0009-2614(99)00888-X  0.96
1996 Elofsson A, Nilsson L. A 1.2 ns molecular dynamics simulation of the ribonuclease T1-3′-guanosine monophosphate complex Journal of Physical Chemistry. 100: 2480-2488. DOI: 10.1021/Jp952517G  0.96
1993 Elofsson A, Nilsson L. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. Journal of Molecular Biology. 233: 766-80. PMID 8411178 DOI: 10.1006/Jmbi.1993.1551  0.96
1993 Whitley P, Nilsson L, von Heijne G. Three-dimensional model for the membrane domain of Escherichia coli leader peptidase based on disulfide mapping. Biochemistry. 32: 8534-9. PMID 8357800 DOI: 10.1021/Bi00084A020  0.64
1993 Elofsson A, Kulinski T, Rigler R, Nilsson L. 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. Proteins. 17: 161-75. PMID 8265564 DOI: 10.1002/Prot.340170206  0.96
1993 Vogel H, Nilsson L, Rigler R, Meder S, Boheim G, Beck W, Kurth HH, Jung G. Structural fluctuations between two conformational states of a transmembrane helical peptide are related to its channel-forming properties in planar lipid membranes. European Journal of Biochemistry / Febs. 212: 305-13. PMID 7680310 DOI: 10.1111/J.1432-1033.1993.Tb17663.X  0.96
1992 Patel N, Berglund H, Nilsson L, Rigler R, McLaughlin LW, Gräslund A. Thermodynamics of interaction of a fluorescent DNA oligomer with the anti-tumour drug netropsin. European Journal of Biochemistry / Febs. 203: 361-6. PMID 1310467 DOI: 10.1111/J.1432-1033.1992.Tb16558.X  0.96
1991 Elofsson A, Rigler R, Nilsson L, Roslund J, Krause G, Holmgren A. Motion of aromatic side chains, picosecond fluorescence, and internal energy transfer in Escherichia coli thioredoxin studied by site-directed mutagenesis, time-resolved fluorescence spectroscopy, and molecular dynamics simulations. Biochemistry. 30: 9648-56. PMID 1911751 DOI: 10.1021/Bi00104A012  1
1991 Patel N, Graslund A, Berglund H, Nilsson L, Rigler R, McLaughlin LW. Interaction of a minor groove binder with a fluorescent DNA oligomer containing the Eco RI recognition sequence Nucleosides and Nucleotides. 10: 547-548. DOI: 10.1080/07328319108046523  0.96
1990 Elofsson A, Nilsson L, Rigler R. Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations. International Journal of Peptide and Protein Research. 36: 297-301. PMID 1980672 DOI: 10.1111/J.1399-3011.1990.Tb00982.X  0.96
1989 Nordlund TM, Andersson S, Nilsson L, Rigler R, Gräslund A, McLaughlin LW. Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry. 28: 9095-103. PMID 2605243 DOI: 10.1021/Bi00449A021  0.96
1989 MacKerell AD, Nilsson L, Rigler R, Heinemann U, Saenger W. Molecular dynamics simulations of ribonuclease T1: comparison of the free enzyme and the 2' GMP-enzyme complex. Proteins. 6: 20-31. PMID 2558378 DOI: 10.1002/Prot.340060103  0.96
1988 Gavel Y, Nilsson L, von Heijne G. Mitochondrial targeting sequences. Why 'non-amphiphilic' peptides may still be amphiphilic. Febs Letters. 235: 173-7. PMID 3402595 DOI: 10.1016/0014-5793(88)81257-2  0.8
1988 MacKerell AD, Nilsson L, Rigler R, Saenger W. Molecular dynamics simulations of ribonuclease T1: analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme. Biochemistry. 27: 4547-56. PMID 3139027 DOI: 10.1021/Bi00412A049  0.96
1988 Vogel H, Nilsson L, Rigler R, Voges KP, Jung G. Structural fluctuations of a helical polypeptide traversing a lipid bilayer. Proceedings of the National Academy of Sciences of the United States of America. 85: 5067-71. PMID 3079525 DOI: 10.1073/Pnas.85.14.5067  0.96
1988 MacKerell AD, Rigler R, Nilsson L, Heinemann U, Saenger W. Molecular dynamics simulations of ribonuclease T1. Effect of solvent on the interaction with 2'GMP. European Biophysics Journal : Ebj. 16: 287-97. PMID 2853669 DOI: 10.1007/BF00254065  0.96
1987 MacKerell AD, Rigler R, Nilsson L, Hahn U, Saenger W. Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1. Biophysical Chemistry. 26: 247-61. PMID 3111558 DOI: 10.1016/0301-4622(87)80027-3  0.96
1983 Nilsson L, Rigler R, Wintermeyer W. The influence of spermine on the structural dynamics of yeast tRNAPhe. Biochimica Et Biophysica Acta. 740: 460-5. PMID 6349691 DOI: 10.1016/0167-4781(83)90095-7  0.96
1982 Nilsson L, Rigler R, Laggner P. Structural variability of tRNA: small-angle x-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex. Proceedings of the National Academy of Sciences of the United States of America. 79: 5891-5. PMID 6764532 DOI: 10.1073/Pnas.79.19.5891  0.96
1981 Rigler R, Nilsson L, Wintermeyer W, Pachmann U, Zachau HG. Conformational states of yeast tRNA Phe in the complex with cognate and non cognate synthetases. Nucleic Acids Research. 9: 1031-44. PMID 7232205 DOI: 10.1093/Nar/9.4.1031  0.96
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