Lennart Nilsson

发表

How Thioredoxin Dissociates Its Mixed Disulfide

Goedele Roos, Nicolas Foloppe, Koen Van Laer, 2009, PLoS Comput. Biol..

Structural dynamics of DNA sensed by fluorescence from chemically modified bases

Lennart Nilsson, Thomas M. Nordlund, Pengguang Wu, 1990, Photonics West - Lasers and Applications in Science and Engineering.

Additive CHARMM force field for naturally occurring modified ribonucleotides

Alexander D. MacKerell, You Xu, Lennart Nilsson, 2016, J. Comput. Chem..

A Highly Efficient Ab Initio Tight-Binding-Like Approximate Density-Functional Quantum Mechanical Method

Lennart Nilsson, Aatto Laaksonen, Yaoquan Tu, 2006, PARA.

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids

Lennart Nilsson, Alessandra Villa, Yossa Dwi Hartono, 2018, J. Chem. Inf. Model..

Some practical aspects of free energy calculations from molecular dynamics simulation

Lennart Nilsson, Srikanta Sen, 1999, J. Comput. Chem..

Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all‐atom additive force field for RNA

Alexander D. MacKerell, Lennart Nilsson, U. Deva Priyakumar, 2011, J. Comput. Chem..

Structure and dynamics of liquid water with different long‐range interaction truncation and temperature control methods in molecular dynamics simulations

Lennart Nilsson, Pekka Mark, L. Nilsson, 2002, J. Comput. Chem..

Advances in biomolecular simulations: methodology and recent applications

Lennart Nilsson, Jan Norberg, L. Nilsson, 2003, Quarterly Reviews of Biophysics.

Improved precision and efficiency of free energy calculations for small systems using λ‐scaled atomic masses and separating conformational and transformational sampling

Lennart Nilsson, Peter Carlsson, L. Nilsson, 2003, J. Comput. Chem..

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields

Lennart Nilsson, Joanna Sarzynska, Ansuman Lahiri, 2014, J. Chem. Inf. Model..

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid

You Xu, Lennart Nilsson, Alessandra Villa, 2017, J. Comput. Chem..

Quantitative confocal fluorescence microscopy of dynamic processes by multifocal fluorescence correlation spectroscopy

Simone Tisa, Lennart Nilsson, Per Thyberg, 2015, European Conference on Biomedical Optics.

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations

Lennart Nilsson, L. Nilsson, 2009, J. Comput. Chem..

Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides.

Nicolas Foloppe, Lennart Nilsson, N. Foloppe, 2005, The journal of physical chemistry. B.

Analysis of the Stability and Flexibility of RNA Complexes Containing Bulge Loops of Different Sizes

Lennart Nilsson, L. Nilsson, R. Strömberg, 2008, Journal of biomolecular structure & dynamics.

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization.

Lennart Nilsson, L. Nilsson, K. Koehler, 2005, Molecular endocrinology.

Mycoredoxin‐1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria

Goedele Roos, Nicolas Foloppe, Lennart Nilsson, 2012, Molecular microbiology.

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

Lennart Nilsson, M. Ohman, L. Nilsson, 2005, RNA.

Urea parametrization for molecular dynamics simulations

Lennart Nilsson, L. Nilsson, Ana Caballero-Herrera, 2006 .

Molecular dynamics applied to nucleic acids.

Lennart Nilsson, Jan Norberg, L. Nilsson, 2002, Accounts of chemical research.

Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution

Lennart Nilsson, Tadeusz Kulinski, Joanna Sarzynska, 2007 .

Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

Lennart Nilsson, Vineet Pande, L. Nilsson, 2008, Nucleic acids research.

Stabilization of the catalytic thiolate in a mammalian glutaredoxin: structure, dynamics and electrostatics of reduced pig glutaredoxin and its mutants.

Nicolas Foloppe, Lennart Nilsson, N. Foloppe, 2007, Journal of molecular biology.

Structural insights into the DNA-binding specificity of E2F family transcription factors

Lennart Nilsson, Kashyap Dave, Jussi Taipale, 2015, Nature Communications.

Molecular Dynamics Simulations of the Ala-Pro Dipeptide in Water: Conformational Dynamics of Trans and Cis Isomers Using Different Water Models

Lennart Nilsson, Pekka Mark, 2001 .

Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations

Lennart Nilsson, Pemra Doruker, L. Nilsson, 2006, Journal of biomolecular structure & dynamics.

Implicit Solvent Models and Stabilizing Effects of Mutations and Ligands on the Unfolding of the Amyloid β-Peptide Central Helix.

Lennart Nilsson, L. Nilsson, Mika Ito, 2013, Journal of chemical theory and computation.

Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima.

Lennart Nilsson, L. Nilsson, R. Ladenstein, 2007, Biochemistry.

The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues.

Nicolas Foloppe, Lennart Nilsson, N. Foloppe, 2004, Structure.

Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

Lennart Nilsson, Alessandra Villa, L. Nilsson, 2013, RNA.

Thermal unfolding simulations of a multimeric protein—Transition state and unfolding pathways

Lennart Nilsson, Jianxin Duan, L. Nilsson, 2005, Proteins.

Exploring the idea of self-guided dynamics

Lennart Nilsson, Aatto Laaksonen, Ansuman Lahiri, 2001 .

Stacking Free Energy Profiles for All 16 Natural Ribodinucleoside Monophosphates in Aqueous Solution

Lennart Nilsson, Jan Norberg, L. Nilsson, 1995 .

Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2

Lennart Nilsson, Jan Norberg, L. Nilsson, 1996 .

Molecular origin of time-dependent fluorescence shifts in proteins.

Lennart Nilsson, L. Nilsson, B. Halle, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study.

Alexander D. MacKerell, Nicolas Foloppe, Lennart Nilsson, 2002, Biophysical journal.

Temperature dependence of the stacking propensity of adenylyl-3',5'-adenosine

Lennart Nilsson, Jan Norberg, 1995 .

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome.

Lennart Nilsson, L. Nilsson, Olof Allnér, 2011, RNA.

Molecular dynamics simulation of galanin in aqueous and nonaqueous solution

Lennart Nilsson, Rudolf Rigler, L. Nilsson, 1992 .

Effect of G40R mutation on the binding of human SRY protein to DNA: A molecular dynamics view

Lennart Nilsson, Yun Tang, Yun Tang, 1999, Proteins.

Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics.

Lennart Nilsson, L. Nilsson, P. Carlsson, 2006, Biophysical journal.

Structure, Dynamics and Function of Biomolecules

Lennart Nilsson, Astrid Gräslund, Rudolf Rigler, 1987 .

Empirical energy functions for energy minimization and dynamics of nucleic acids

Lennart Nilsson, Martin Karplus, M. Karplus, 1986 .

Functional Fluorescence Microscopy Imaging (fFMI). Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells.

Simone Tisa, Lennart Nilsson, Per Thyberg, 2019, Analytical chemistry.

The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43.

Lennart Nilsson, Amir Porat, Jon Beckwith, 2007, Biochemistry.

Rigidity versus flexibility: the dilemma of understanding protein thermal stability

Lennart Nilsson, Andrey Karshikoff, L. Nilsson, 2015, The FEBS journal.

Computational studies of LXR molecular interactions reveal an allosteric communication pathway

Lennart Nilsson, L. Nilsson, Sofia Burendahl, 2012, Proteins.

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.

Lennart Nilsson, Tadeusz Kulinski, Joanna Sarzynska, 2003, Biophysical journal.

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations.

Yuichi Inadomi, Lennart Nilsson, Umpei Nagashima, 2007, The journal of physical chemistry. B.

Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures

Charles L. Brooks, Lennart Nilsson, C. Brooks, 1993 .

CONFORMATIONAL FREE ENERGY LANDSCAPE OF APAPA FROM MOLECULAR DYNAMICS SIMULATIONS

Lennart Nilsson, Jan Norberg, L. Nilsson, 1996 .

Ligand unbinding from the estrogen receptor: A computational study of pathways and ligand specificity

Lennart Nilsson, L. Nilsson, Sofia Burendahl, 2009, Proteins.

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

Lennart Nilsson, Ian S. Haworth, Ite A. Laird-Offringa, 2006, Nucleic acids research.

Molecular Dynamics Study of Intrinsic Stability in Six RNA Terminal Loop Motifs

Lennart Nilsson, L. Nilsson, B. Nyström, 2007, Journal of biomolecular structure & dynamics.

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations.

Lennart Nilsson, Alessandra Villa, L. Nilsson, 2012, Journal of chemical theory and computation.