| Year |
Citation |
Score |
| 2023 |
Tamez A, Nilsson L, Mihailescu MR, Evanseck JD. Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation. Journal of Chemical Theory and Computation. PMID 37195939 DOI: 10.1021/acs.jctc.2c01163 |
0.319 |
|
| 2019 |
Nilsson L, Villa A. Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy. Methods in Molecular Biology (Clifton, N.J.). 2036: 113-126. PMID 31410793 DOI: 10.1007/978-1-4939-9670-4_6 |
0.384 |
|
| 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 |
0.528 |
|
| 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 |
0.384 |
|
| 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 |
0.321 |
|
| 2018 |
Salamanova E, Costeira-Paulo J, Han KH, Kim DH, Nilsson L, Wright APH. A subset of functional adaptation mutations alter propensity for α-helical conformation in the intrinsically disordered glucocorticoid receptor tau1core activation domain. Biochimica Et Biophysica Acta. PMID 29550429 DOI: 10.1016/J.Bbagen.2018.03.015 |
0.301 |
|
| 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 |
0.329 |
|
| 2017 |
Hartono YD, Ito M, Villa A, Nilsson L. A 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. The Journal of Physical Chemistry. B. PMID 29260566 DOI: 10.1021/Acs.Jpcb.7B10878 |
0.375 |
|
| 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 |
0.37 |
|
| 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 |
0.336 |
|
| 2016 |
Juneja A, Nilsson L, Villa A. Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus. Biophysical Chemistry. 218: 7-13. PMID 27564708 DOI: 10.1016/J.Bpc.2016.08.001 |
0.381 |
|
| 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 |
0.571 |
|
| 2016 |
Xu Y, Vanommeslaeghe K, Aleksandrov A, MacKerell AD, Nilsson L. Additive CHARMM force field for naturally occurring modified ribonucleotides. Journal of Computational Chemistry. PMID 26841080 DOI: 10.1002/Jcc.24307 |
0.523 |
|
| 2015 |
Morgunova E, Yin Y, Jolma A, Dave K, Schmierer B, Popov A, Eremina N, Nilsson L, Taipale J. Structural insights into the DNA-binding specificity of E2F family transcription factors. Nature Communications. 6: 10050. PMID 26632596 DOI: 10.1038/Ncomms10050 |
0.338 |
|
| 2015 |
Nilsson L. Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules. Biophysical Journal. 108: 2755-6. PMID 26083911 DOI: 10.1016/J.Bpj.2015.05.007 |
0.332 |
|
| 2015 |
Karshikoff A, Nilsson L, Ladenstein R. Rigidity versus flexibility: the dilemma of understanding protein thermal stability. The Febs Journal. PMID 26074325 DOI: 10.1111/Febs.13343 |
0.359 |
|
| 2015 |
Allnér O, Foloppe N, Nilsson L. Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations. The Journal of Physical Chemistry. B. 119: 1114-28. PMID 25350574 DOI: 10.1021/Jp506609G |
0.405 |
|
| 2015 |
Krmpot AJ, Nikolić SN, Vitali M, Papadopoulos DK, Oasa S, Thyberg P, Tisa S, Kinjo M, Nilsson L, Gehring WJ, Terenius L, Rigler R, Vukojević V. Quantitative confocal fluorescence microscopy of dynamic processes by multifocal fluorescence correlation spectroscopy Progress in Biomedical Optics and Imaging - Proceedings of Spie. 9536. DOI: 10.1117/12.2183935 |
0.46 |
|
| 2015 |
Xu Y, Nilsson L, MacKerrel AD. An Additive Charmm Force Field for Modified Nucleic Acids Biophysical Journal. 108: 235a-236a. DOI: 10.1016/J.Bpj.2014.11.1302 |
0.363 |
|
| 2014 |
Juneja A, Villa A, Nilsson L. Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics. Journal of Chemical Theory and Computation. 10: 3532-40. PMID 26588317 DOI: 10.1021/Ct500203M |
0.342 |
|
| 2014 |
Esguerra M, Nilsson L, Villa A. Triple helical DNA in a duplex context and base pair opening. Nucleic Acids Research. 42: 11329-38. PMID 25228466 DOI: 10.1093/Nar/Gku848 |
0.355 |
|
| 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 |
0.35 |
|
| 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 |
0.349 |
|
| 2014 |
Zamora-Ros R, Luján-Barroso L, Bueno-de-Mesquita HB, Dik VK, Boeing H, Steffen A, Tjønneland A, Olsen A, Bech BH, Overvad K, Boutron-Ruault MC, Racine A, Fagherazzi G, Kuhn T, Katzke V, ... ... Nilsson L, et al. Tea and coffee consumption and risk of esophageal cancer: the European prospective investigation into cancer and nutrition study. International Journal of Cancer. Journal International Du Cancer. 135: 1470-9. PMID 24535727 DOI: 10.1002/ijc.28789 |
0.411 |
|
| 2014 |
Uyar A, Pande V, Mura C, McCammon JA, Doruker P, Nilsson L. Assessing Dynamic Features of NF-κB via Molecular Dynamics Simulations and Elastic Network Model Biophysical Journal. 106: 252a. DOI: 10.1016/J.Bpj.2013.11.1482 |
0.366 |
|
| 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: 834-46. PMID 26589074 DOI: 10.1021/Ct300941V |
0.316 |
|
| 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 |
0.332 |
|
| 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 |
0.41 |
|
| 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 |
0.344 |
|
| 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 |
0.306 |
|
| 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 |
0.351 |
|
| 2012 |
Samuelsson A, Isaksson B, Chabok A, Jonasson J, Nilsson LE, Eriksson O, Hanberger H. Changes in the aerobic faecal flora of patients treated with antibiotics for acute intra-abdominal infection. Scandinavian Journal of Infectious Diseases. 44: 820-7. PMID 22831634 DOI: 10.3109/00365548.2012.695455 |
0.412 |
|
| 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 |
0.533 |
|
| 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 |
0.377 |
|
| 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 |
0.322 |
|
| 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 |
0.363 |
|
| 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 |
0.349 |
|
| 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 |
0.341 |
|
| 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 |
0.533 |
|
| 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 |
0.362 |
|
| 2010 |
Juneja A, Numata J, Nilsson L, Knapp EW. Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol. Journal of Chemical Theory and Computation. 6: 1871-83. PMID 26615846 DOI: 10.1021/Ct100075M |
0.365 |
|
| 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 |
0.3 |
|
| 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 |
0.34 |
|
| 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 |
0.345 |
|
| 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 |
0.536 |
|
| 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 |
0.304 |
|
| 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 |
0.318 |
|
| 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 |
0.324 |
|
| 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 |
0.372 |
|
| 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 |
0.385 |
|
| 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 |
0.33 |
|
| 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 |
0.563 |
|
| 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 |
0.317 |
|
| 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 |
0.387 |
|
| 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 |
0.318 |
|
| 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 |
0.411 |
|
| 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 |
0.359 |
|
| 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 |
0.332 |
|
| 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 |
0.385 |
|
| 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 |
0.418 |
|
| 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 |
0.315 |
|
| 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 |
0.402 |
|
| 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 |
0.344 |
|
| 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 |
0.326 |
|
| 2006 |
Watanabe T, Inadomi Y, Fukuzawa K, Tanaka S, Nakano T, Nilsson L, Nagashima U. S1d1-7 DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method(S1-d1: "Structure and Function of Weak Interactions in Protein Molecules",Symposia,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46: S108. DOI: 10.2142/Biophys.46.S108_1 |
0.312 |
|
| 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 |
0.391 |
|
| 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 |
0.401 |
|
| 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 |
0.365 |
|
| 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 |
0.323 |
|
| 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 |
0.347 |
|
| 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 |
0.345 |
|
| 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 |
0.368 |
|
| 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 |
0.314 |
|
| 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 |
0.318 |
|
| 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 |
0.376 |
|
| 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 |
0.357 |
|
| 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 |
0.304 |
|
| 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 |
0.392 |
|
| 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 |
0.338 |
|
| 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 |
0.424 |
|
| 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 |
0.346 |
|
| 2002 |
Norberg J, Nilsson L. Molecular dynamics applied to nucleic acids Accounts of Chemical Research. 35: 465-472. PMID 12069632 DOI: 10.1021/Ar010026A |
0.361 |
|
| 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 |
0.538 |
|
| 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 |
0.365 |
|
| 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 |
0.367 |
|
| 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 |
0.346 |
|
| 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 |
0.56 |
|
| 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 |
0.384 |
|
| 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 |
0.405 |
|
| 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 |
0.37 |
|
| 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 |
0.337 |
|
| 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 |
0.308 |
|
| 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 |
0.407 |
|
| 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 |
0.356 |
|
| 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 |
0.387 |
|
| 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 |
0.342 |
|
| 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 |
0.377 |
|
| 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 |
0.398 |
|
| 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 |
0.373 |
|
| 1999 |
Tang Y, Nilsson L. Effect of G40R mutation on the binding of human SRY protein to DNA: a molecular dynamics view. Proteins. 35: 101-13. PMID 10090290 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<101::Aid-Prot10>3.0.Co;2-5 |
0.381 |
|
| 1999 |
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. European Biophysics Journal : Ebj. 28: 102-11. PMID 10028235 DOI: 10.1007/S002490050189 |
0.371 |
|
| 1999 |
Manoj N, Srinivas VR, Surolia A, Vijayan M, Suguna K, Ravishankar R, Schwarzenbacher R, Zeth K, Diederichs, Kostner GM, Gries A, Laggner P, Prassl R, Madhusudan, Akamine P, ... ... Nilsson L, et al. Contributory presentations/posters Journal of Biosciences. 24: 33-198. DOI: 10.1007/Bf02989373 |
0.469 |
|
| 1999 |
Sen S, Nilsson L. Some practical aspects of free energy calculations from molecular dynamics simulation Journal of Computational Chemistry. 20: 877-885. DOI: 10.1002/(Sici)1096-987X(199906)20:8<877::Aid-Jcc12>3.0.Co;2-O |
0.362 |
|
| 1998 |
Eriksson MA, Nilsson L. Structural and dynamic effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain. Protein Engineering. 11: 589-600. PMID 9740378 DOI: 10.1093/Protein/11.7.589 |
0.371 |
|
| 1998 |
Tang Y, Nilsson L. Interaction of human SRY protein with DNA: a molecular dynamics study. Proteins. 31: 417-33. PMID 9626701 DOI: 10.1002/(Sici)1097-0134(19980601)31:4<417::Aid-Prot8>3.0.Co;2-E |
0.353 |
|
| 1998 |
Lamminmäki U, Villoutreix BO, Jauria P, Saviranta P, Vihinen M, Nilsson L, Teleman O, Lövgren T. Structural analysis of an anti-estradiol antibody. Molecular Immunology. 34: 1215-26. PMID 9566768 DOI: 10.1016/S0161-5890(97)00085-0 |
0.315 |
|
| 1998 |
Norberg J, Nilsson L. Solvent influence on base stacking. Biophysical Journal. 74: 394-402. PMID 9449339 DOI: 10.1016/S0006-3495(98)77796-3 |
0.3 |
|
| 1998 |
Sen S, Nilsson L. Molecular Dynamics of Duplex Systems Involving PNA: Structural and Dynamical Consequences of the Nucleic Acid Backbone Journal of the American Chemical Society. 120: 619-631. DOI: 10.1021/Ja972234X |
0.381 |
|
| 1997 |
Lahiri A, Nilsson L. Properties of dianionic oxyphosphorane intermediates from hybrid QM/MM simulation: implications for ribozyme reactions Journal of Molecular Structure: Theochem. 419: 51-55. DOI: 10.1016/S0166-1280(97)00180-2 |
0.324 |
|
| 1996 |
Norberg J, Nilsson L. Glass transition in DNA from molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 93: 10173-6. PMID 8816771 DOI: 10.1073/Pnas.93.19.10173 |
0.326 |
|
| 1996 |
Norberg J, Nilsson L. Internal mobility of the oligonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations. Journal of Biomolecular Nmr. 7: 305-14. PMID 8765737 DOI: 10.1007/Bf00200432 |
0.328 |
|
| 1996 |
Skoging U, Vihinen M, Nilsson L, Liljeström P. Aromatic interactions define the binding of the alphavirus spike to its nucleocapsid. Structure. 4: 519-529. PMID 8736551 DOI: 10.1016/S0969-2126(96)00058-5 |
0.308 |
|
| 1996 |
Norberg J, Nilsson L. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates. Biophysical Journal. 69: 2277-85. PMID 8599635 DOI: 10.1016/S0006-3495(95)80098-6 |
0.362 |
|
| 1996 |
Norberg J, Nilsson L. Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2 The Journal of Chemical Physics. 104: 6052-6057. DOI: 10.1063/1.471341 |
0.34 |
|
| 1996 |
Norberg J, Nilsson L. Conformational Free Energy Landscape of ApApA from Molecular Dynamics Simulations The Journal of Physical Chemistry. 100: 2550-2554. DOI: 10.1021/Jp952950Q |
0.379 |
|
| 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 |
0.632 |
|
| 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. 21: 57-67. PMID 7716169 DOI: 10.1002/Prot.340210107 |
0.33 |
|
| 1995 |
Eriksson MA, Härd T, Nilsson L. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophysical Journal. 68: 402-26. PMID 7696496 DOI: 10.1016/S0006-3495(95)80203-1 |
0.359 |
|
| 1995 |
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. Journal of Molecular Biology. 253: 453-72. PMID 7473727 DOI: 10.1006/Jmbi.1995.0566 |
0.421 |
|
| 1995 |
Norberg J, Nilsson L. NMR Relaxation Times, Dynamics, and Hydration of a Nucleic Acid Fragment from Molecular Dynamics Simulations The Journal of Physical Chemistry. 99: 14876-14884. DOI: 10.1021/J100040A043 |
0.378 |
|
| 1994 |
Eriksson MA, Berglund H, Härd T, Nilsson L. A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain. Proteins. 17: 375-90. PMID 8108380 DOI: 10.1002/Prot.340170406 |
0.392 |
|
| 1994 |
Norberg J, Nilsson L. Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics. Biophysical Journal. 67: 812-24. PMID 7948694 DOI: 10.1016/S0006-3495(94)80541-7 |
0.387 |
|
| 1994 |
Norberg J, Nilsson L. High-pressure molecular dynamics of a nucleic acid fragment Chemical Physics Letters. 224: 219-224. DOI: 10.1016/0009-2614(94)00507-9 |
0.337 |
|
| 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 |
0.613 |
|
| 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 |
0.691 |
|
| 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 |
0.554 |
|
| 1993 |
Elofsson A, Nilsson L. Free Energy Perturbations in Ribonuclease T1Substrate Binding. A Study of the Influence of Simulation Length, Internal Degrees of Freedom and Structure in Free Energy Perturbations Molecular Simulation. 10: 255-276. DOI: 10.1080/08927029308022168 |
0.603 |
|
| 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 |
0.551 |
|
| 1992 |
De Loof H, Nilsson L, Rigler R. Molecular dynamics simulation of galanin in aqueous and nonaqueous solution Journal of the American Chemical Society. 114: 4028-4035. DOI: 10.1021/Ja00037A002 |
0.583 |
|
| 1992 |
Wennerberg A, De Loof H, Kulinski T, Elofsson A, Nilsson L, Rigler R. Study of the distribution function of the three-dimensional structures of rat galanin determined by two-dimensional 1H NMR, distance geometry calculations, molecular dynamics and energy transfer measurements Regulatory Peptides. 37: S175. DOI: 10.1016/0167-0115(92)91030-4 |
0.664 |
|
| 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 |
0.694 |
|
| 1991 |
Härd T, Nilsson L. Free Energy Calculations Predict Sequence Specificity In DNA-drug Complexes Nucleosides and Nucleotides. 10: 701-709. DOI: 10.1080/07328319108046577 |
0.349 |
|
| 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 |
0.534 |
|
| 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 |
0.708 |
|
| 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 |
0.584 |
|
| 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 |
0.685 |
|
| 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 |
0.691 |
|
| 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 |
0.584 |
|
| 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 |
0.652 |
|
| 1988 |
Elofsson A, Ghosh I, MacKerell A, Nilsson L, Rigler R. Molecular structure, dynamics and function of signal and transmitter peptides Regulatory Peptides. 22: 63. DOI: 10.1016/0167-0115(88)90283-2 |
0.661 |
|
| 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 |
0.664 |
|
| 1986 |
Nilsson L, Clore GM, Gronenborn AM, Brünger AT, Karplus M. Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2. Journal of Molecular Biology. 188: 455-75. PMID 3016285 DOI: 10.1016/0022-2836(86)90168-3 |
0.346 |
|
| 1986 |
Nilsson L, Karplus M. Empirical energy functions for energy minimization and dynamics of nucleic acids Journal of Computational Chemistry. 7: 591-616. DOI: 10.1002/Jcc.540070502 |
0.349 |
|
| 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 |
0.519 |
|
| 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 |
0.521 |
|
| 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 |
0.553 |
|
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