Publications from

Total publications from unit:

2021

1.

Dennis V. Pedersen, Martin Nors Pedersen, Sofia M. M. Mazarakis, Yong Wang, Kresten Lindorff-Larsen, Lise Arleth and Gregers R. Andersen. (2021) Properdin oligomers adopt rigid extended conformations supporting function eLife 10.

2.

Erik W. Martin, F. Emil Thomasen, Nicole M. Milkovic, Matthew J. Cuneo, Christy R. Grace, Amanda Nourse, Kresten Lindorff-Larsen and Tanja Mittag. (2021) Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation Nucleic Acids Research 49(5):2931-2945.

3.

Giulio Tesei, João M. Martins, Micha B. A. Kunze, Yong Wang, Ramon Crehuet and Kresten Lindorff-Larsen. (2021) DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles PLOS Computational Biology 17(1).

4.

Kresten Lindorff-Larsen and Kaare Teilum. (2021) Linking thermodynamics and measurements of protein stability Protein engineering, design & selection : PEDS 34.

5.

Stefan Hervø-Hansen, Casper Højgaard, Kristoffer Enøe Johansson, Yong Wang, Khadija Wahni, David Young, Joris Messens, Kaare Teilum, Kresten Lindorff-Larsen and Jakob Rahr Winther. (2021) Charge Interactions in a Highly Charge-Depleted Protein Journal of the American Chemical Society 143(6):2500-2508.

2020

6.

Tone Bengtsen, Søren Roi Midtgaard, Viktor Lindahl Holm, Lisbeth Ravnkilde Kjølbye, Nicolai Tidemand Johansen, Giulio Tesei, Sandro Bottaro, Birgit Schiøtt, Lise Arleth and Kresten Lindorff-Larsen. (2020) Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations. eLife 9.

7.

Lise Arleth, Nicolai T. Johansen, Tone Bengtsen, Andreas Haahr Larsen, Frederik Tidemand, Thomas Pomorski and Kresten Lindorff-Larsen. (2020) Small-angle Neutron Scattering Shows that the Solution Structures of the Bacterial Mg2+-Channel CorA are Overall Similar with and without Mg2+ Bound Biophysical Journal 118:12A-12A.

8.

Amanda B. Abildgaard, Sarah K. Gersing, Sven Larsen-Ledet, Sofie V. Nielsen, Amelie Stein, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2020) Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome Biomolecules 10(8).

9.

Amanda B. Abildgaard, Sarah K. Gersing, Sven Larsen-Ledet, Sofie V. Nielsen, Amelie Stein, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2020) Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome Biomolecules 10(8).

10.

Andreas Haahr Larsen, Yong Wang, Sandro Bottaro, Sergei Grudinin, Lise Arleth and Kresten Lindorff-Larsen. (2020) Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution P L o S Computational Biology 16(4).

11.

Helena Gásdal Karstensen, Nanna Dahl Rendtorff, Lone Sandbjerg Hindbæk, Roberto Colombo, Amelie Stein, Niels Holtum Birkebæk, Rasmus Hartmann-Petersen, Kresten Lindorff-Larsen, Allan Thomas Højland, Michael Bjørn Petersen and Lisbeth Tranebjærg. (2020) Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome European Journal of Medical Genetics 63(3).

12.

Iva Sucec, Yong Wang, Ons Dakhlaoui, Katharina Weinhäupl, Tobias Jores, Doriane Costa, Audrey Hessel, Martha Brennich, Doron Rapaport, Kresten Lindorff-Larsen, Beate Bersch and Paul Schanda. (2020) Structural basis of client specificity in mitochondrial membrane-protein chaperones Science Advances 6(51).

13.

James S. Fraser, Kresten Lindorff-Larsen and Massimiliano Bonomi. (2020) What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? Journal of Chemical Information and Modeling 60(5):2410-2412.

14.

João Henriques and Kresten Lindorff-Larsen. (2020) Protein Dynamics Enables Phosphorylation of Buried Residues in Cdk2/Cyclin-A-Bound p27 Biophysical Journal 119(10):2010-2018.

15.

Lene Clausen, Amelie Stein, Martin Grønbæk-Thygesen, Lasse Nygaard, Cecilie L. Søltoft, Sofie V. Nielsen, Michael Lisby, Tommer Ravid, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2020) Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation PLOS Genetics 16(11).

16.

Louise Hamborg, Emma Wenzel Horsted, Kristoffer Enøe Johansson, Martin Willemoës, Kresten Lindorff-Larsen and Kaare Teilum. (2020) Global analysis of protein stability by temperature and chemical denaturation Analytical Biochemistry 605.

17.

Michael Maglegaard Jepsen, Douglas M. Fowler, Rasmus Hartmann-Petersen, Amelie Stein and Kresten Lindorff-Larsen. (2020) Classifying disease-associated variants using measures of protein activity and stability False:91-107.

18.

Mustapha Carab Ahmed, Ramon Crehuet and Kresten Lindorff-Larsen. (2020) Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins False:429-445.

19.

Sandro Bottaro, Parker J. Nichols, Beat Vögeli, Michele Parrinello and Kresten Lindorff-Larsen. (2020) Integrating NMR and simulations reveals motions in the UUCG tetraloop Nucleic Acids Research 48(11):5839-5848.

20.

Sandro Bottaro, Tone Bengtsen and Kresten Lindorff-Larsen. (2020) Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach False:219-240.

21.

Simone Orioli, Andreas Haahr Larsen, Sandro Bottaro and Kresten Lindorff-Larsen. (2020) How to learn from inconsistencies: Integrating molecular simulations with experimental data False:123-176.

22.

Sofie V. Nielsen, Signe M. Schenstrøm, Caspar E. Christensen, Amelie Stein, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2020) Protein destabilization and degradation as a mechanism for hereditary disease False:111-125.

2019

23.

Michael Lückmann, Mette Trauelsen, Marie A Bentsen, Tinne A D Nissen, Joao Martins, Zohreh Fallah, Mads M Nygaard, Elena Papaleo, Kresten Lindorff-Larsen, Thue W Schwartz and Thomas M Frimurer. (2019) Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1 Proceedings of the National Academy of Sciences of the United States of America 116(14):7123-7128.

24.

Albert Escobedo, Busra Topal, Micha B. A. Kunze, Juan Aranda, Giulio Chiesa, Daniele Mungianu, Ganeko Bernardo-Seisdedos, Bahareh Eftekharzadeh, Margarida Gairí, Roberta Pierattelli, Isabella C. Felli, Tammo Diercks, Oscar Millet, Jesús García, Modesto Orozco, Ramon Crehuet, Kresten Lindorff-Larsen and Xavier Salvatella. (2019) Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor Nature Communications 10.

25.

Amanda B. Abildgaard, Amelie Stein, Sofie V. Nielsen, Katrine Schultz-Knudsen, Elena Papaleo, Amruta Shrikhande, Eva R Hoffmann, Inge Bernstein, Anne-Marie Gerdes, Masanobu Takahashi, Chikashi Ishioka, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2019) Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome eLife 8.

26.

Amelie Stein, Douglas M. Fowler, Rasmus Hartmann-Petersen and Kresten Lindorff-Larsen. (2019) Biophysical and Mechanistic Models for Disease-Causing Protein Variants Trends in Biochemical Sciences 44(7):575-588.

27.

Andrea Cesari, Sandro Bottaro, Kresten Lindorff-Larsen, Pavel Banás, Jiri Sponer and Giovanni Bussi. (2019) Fitting Corrections to an RNA Force Field Using Experimental Data Journal of Chemical Theory and Computation 15(6):3425-3431.

28.

Anne Kathrine Nielsen, Ingvar R. Möller, Yong Wang, Søren G. F. Rasmussen, Kresten Lindorff-Larsen, Kasper D. Rand and Claus J. Loland. (2019) Substrate-induced conformational dynamics of the dopamine transporter Nature Communications 10.

29.

Anne Kathrine Nielsen, Ingvar R. Möller, Yong Wang, Søren G. F. Rasmussen, Kresten Lindorff-Larsen, Kasper D. Rand and Claus J. Loland. (2019) Substrate-induced conformational dynamics of the dopamine transporter Nature Communications 10.

30.

Dennis V. Pedersen, Trine Amalie Fogh Gadeberg, Caroline Thomas, Yong Wang, Nicolas Joram, Rasmus Kjeldsen Jensen, Sofia M. M. Mazarakis, Margot Revel, Carine El Sissy, Steen V. Petersen, Kresten Lindorff-Larsen, Steffen Thiel, Nick Stub Laursen, Véronique Fremeaux-Bacchi and Gregers Rom Andersen. (2019) Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System Frontiers in Immunology 10.

31.

Kresten Lindorff-Larsen. (2019) Dissecting the statistical properties of the linear extrapolation method of determining protein stability Protein engineering, design & selection : PEDS 32(10):471-479.

32.

Lene Clausen, Amanda Bering Abildgaard, Sarah K. Gersing, Amelie Stein, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2019) Protein stability and degradation in health and disease False:61-83.

33.

Martin Cramer Pedersen, Yong Wang, Frederik Grønbæk Tidemand, A. Martel, Kresten Lindorff-Larsen and Lise Arleth. (2019) PSX, Protein-Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates Journal of Applied Crystallography 52(6):1427-1436.

34.

Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth A. Tribello, Pavel Banas, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paolo Carloni, Michele Ceriotti, Andrea Cesari, Haochuan Chen, Wei Chen, Francesco Colizzi, Sandip De, Marco De La Pierre, Davide Donadio, Viktor Drobot, Bernd Ensing, Andrew L. Ferguson, Marta Filizola, James S. Fraser, Haohao Fu, Piero Gasparotto, Francesco Luigi Gervasio, Federico Giberti, Alejandro Gil-Ley, Toni Giorgino, Gabriella T. Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, Kim E. Jelfs, Alexander Jussupow, Evgeny Kirilin, Alessandro Laio, Vittorio Limongelli, Kresten Lindorff-Larsen, Thomas Lohr, Fabrizio Marinelli, Layla Martin-Samos, Matteo Masetti, Ralf Meyer, Angelos Michaelides, Carla Molteni, Tetsuya Morishita, Marco Nava, Cristina Paissoni, Elena Papaleo, Michele Parrinello, Jim Pfaendtner, Pablo Piaggi, GiovanniMaria Piccini, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Davide Provasi, David Quigley, Paolo Raiteri, Stefano Raniolo, Jakub Rydzewski, Matteo Salvalaglio, Gabriele Cesare Sosso, Vojtech Spiwok, Jiri Sponer, David W. H. Swenson, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A. Voth and Andrew White. (2019) Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods 16(8):670-673.

35.

Noureldin Saleh, Yong Wang, Poul Nissen and Kresten Lindorff-Larsen. (2019) Allosteric modulation of the sarcoplasmic reticulum Ca2+ ATPase by thapsigargin via decoupling of functional motions Physical Chemistry Chemical Physics 21(39):21991-21995.

36.

Ramon Crehuet, Pedro J. Buigues, Xavier Salvatella and Kresten Lindorff-Larsen. (2019) Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts Entropy 21(9).

37.

Rasmus Scheller, Amelie Stein, Sofie V. Nielsen, Frederikke I. Marin, Anne-Marie Gerdes, Miriam Di Marco, Elena Papaleo, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2019) Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations Human Mutation 40(4):444-457.

38.

Sandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, Sabine Reisser, Wouter Boomsma and Kresten Lindorff-Larsen. (2019) Barnaba: software for analysis of nucleic acid structures and trajectories RNA 25(2):219-231.

39.

Yong Wang, Noureldin Saleh, Xiakun Chu and Kresten Lindorff-Larsen. (2019) A Multi-State Coarse-Grained Simulation Model Captures Conformational Cycling in P-Type ATPases Biophysical Journal 116:300a.

2018

40.

Joao Henriques, Lise Arleth, Kresten Lindorff-Larsen and Marie Skepo. (2018) On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations Journal of Molecular Biology 430:2521-2539.

41.

Tone Bengtsen, Viktor Lindahl Holm, Søren Roi Midtgaard, Lise Arleth and Kresten Lindorff-Larsen. (2018) A Combined Simulation and SAXS Study of the Dynamics of Lipid Nanodiscs Biophysical Journal 114:559A-559A.

42.

Elena Papaleo, Carlo Camilloni, Kaare Teilum, Michele Vendruscolo and Kresten Lindorff-Larsen. (2018) Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs PeerJ 6:1-24.

43.

Ganesan Senthil Kumar, Michael W. Clarkson, Micha Ben Achim Kunze, Daniele Granata, A. Joshua Wand, Kresten Lindorff-Larsen, Rebecca Page and Wolfgang Peti. (2018) Dynamic activation and regulation of the mitogen-activated protein kinase p38 Proceedings of the National Academy of Sciences of the United States of America 115(18):4655-4660.

44.

Jill J. Bouchard, Joel H. Otero, Daniel C. Scott, Elzbieta Szulc, Erik W. Martin, Nafiseh Sabri, Daniele Granata, Melissa R. Marzahn, Kresten Lindorff-Larsen, Xavier Salvatella, Brenda A. Schulman and Tanja Mittag. (2018) Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments Molecular Cell 72(1):19-36, e1-e8.

45.

Katharina Weinhaupl, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schültze, Tobias Jores, Laura Melchionda, Birgit Schönfisch, Hubert Kalbacher, Beate Bersch, Doron Rapaport, Martha Brennich, Kresten Lindorff-Larsen, Nils Wiedemann and Paul Schanda. (2018) Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space Cell 175(5):1365-1379, e25.

46.

Kristoffer Enøe Johansson and Kresten Lindorff-Larsen. (2018) Structural heterogeneity and dynamics in protein evolution and design Current Opinion in Structural Biology 48:157-163.

47.

Lotte Emilie Boyhus, Mia Danielsen, Nina Smidt Bengtson, Micha Ben Achim Kunze, Xavier Kubiak, Tjerk J. Sminia, Jacob Hartvig Løper, Phuong Thu Tran, Kresten Lindorff-Larsen, Søren G.F. Rasmussen, Jesper Mosolff Mathiesen and Daniel Sejer Pedersen. (2018) Gs protein peptidomimetics as allosteric modulators of the ß2-adrenergic receptor RSC Advances 8(4):2219-2228.

48.

Maher M. Kassem, Lars B. Christoffersen, Andrea Cavalli and Kresten Lindorff-Larsen. (2018) Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts Scientific Reports 8.

49.

Mustapha Carab Hussein Ahmed, Elena Papaleo and Kresten Lindorff-Larsen. (2018) How well do force fields capture the strength of salt bridges in proteins? PeerJ 6.

50.

Paul Santner, Joao Miguel da Silva Martins, Caroline Kampmeyer, Rasmus Hartmann-Petersen, Jonas S. Laursen, Amelie Stein, Christian A Olsen, Isaiah T Arkin, Jakob R. Winther, Martin Willemoës and Kresten Lindorff-Larsen. (2018) Random mutagenesis analysis of the Influenza A M2 proton channel reveals novel resistance mutants Biochemistry 57(41):5957-5968.

51.

Paul Santner, João Miguel da Silva Martins, Jonas S. Laursen, Lars Behrendt, Leise Riber, Christian A Olsen, Isaiah T. Arkin, Jakob R. Winther, Martin Willemoës and Kresten Lindorff-Larsen. (2018) A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel Biochemistry 57(41):5949-5956.

52.

Robert B. Best and Kresten Lindorff-Larsen. (2018) Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level Current Opinion in Structural Biology 49:iv-v.

53.

Sandro Bottaro and Kresten Lindorff-Larsen. (2018) Biophysical experiments and biomolecular simulations: a perfect match? Science 361(6400):355-360.

54.

Sandro Bottaro, Giovanni Bussi, Scott D. Kennedy, Douglas H. Turner and Kresten Lindorff-Larsen. (2018) Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations Science Advances 4(5).

55.

Yong Wang, Katrine Østergaard Bugge, Birthe Brandt Kragelund and Kresten Lindorff-Larsen. (2018) Role of protein dynamics in transmembrane receptor signalling Current Opinion in Structural Biology 48:74-82.

56.

Yong Wang, Omar Valsson, Pratyush Tiwary, Michele Parrinello and Kresten Lindorff-Larsen. (2018) Frequency adaptive metadynamics for the calculation of rare-event kinetics Journal of Chemical Physics 149(7):1-7.

57.

Yong Wang, Pengfei Tian, Wouter Boomsma and Kresten Lindorff-Larsen. (2018) Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias Journal of Physical Chemistry B 122(49):11174-11185.

2017

58.

Ruth Hendus-Altenburger, Matteo Lambrughi, Thilde Bagger Terkelsen, Stine Helene Falsig Pedersen, Elena Papaleo, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2017) A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1) Cellular Signalling 37:40-51.

59.

Yong Wang, João Martins and Kresten Lindorff-Larsen. (2017) Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics Chemical Science 8(9):6466-6473.

60.

Mads Nygaard, Birthe Brandt Kragelund, Elena Papaleo and Kresten Lindorff-Larsen. (2017) An efficient method for estimating the hydrodynamic radius of disordered protein conformations Biophysical Journal 113(3):550-557.

61.

Sandro Bottaro and Kresten Lindorff-Larsen. (2017) Mapping the universe of RNA tetraloop folds Biophysical Journal 113(2):257-267.

62.

Sofie V, Nielsen, Amelie Stein, Alexander B. Dinitzen, Elena Papaleo, Michael H. Tatham, Esben Guldahl Poulsen, Maher Mahmoud Kassem, Lene Juel Rasmussen, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2017) Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations PLoS Genetics 13(4).

63.

Thu Phuong Tran, Christian Ørnbøl Larsen, Tobias Røndbjerg, Martina de Foresta, Micha Ben Achim Kunze, Ales Marek, Jacob Hartvig Løper, Lotte-Emilie Boyhus, Astrid Knuhtsen, Kresten Lindorff-Larsen and Daniel Sejer Pedersen. (2017) Diversity-oriented peptide stapling: a third generation copper-catalysed azide–alkyne cycloaddition stapling and functionalisation strategy Chemistry: A European Journal 23(14):3490-3495.

64.

Meng S. Choy, Yang Li, Luciana E. S. F. Machado, Micha Ben Achim Kunze, Christopher R. Connors, Xingyu Wei, Kresten Lindorff-Larsen, Rebecca Page and Wolfgang Peti. (2017) Conformational rigidity and protein dynamics at distinct timescales regulate PTP1B activity and allostery Molecular Cell 65(4):644-658.

65.

Caroline Kampmeyer, Sofie V. Nielsen, Lene Clausen, Amelie Stein, Anne-Marie Axø Gerdes, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2017) Blocking protein quality control to counter hereditary cancers Genes, Chromosomes & Cancer 56(12):823-831.

66.

Helena Steinocher, Katrine Østergaard Bugge, Louise Fletcher Nikolajsen, Kresten Lindorff-Larsen, Andrew Brooks and Birthe Brandt Kragelund. (2017) Class I Cytokine Receptors: Towards the Inside Biophysical Society. Annual Meeting. Abstracts 112:171A.

2016

67.

Katrine Østergaard Bugge, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2016) Understanding single-pass transmembrane receptor signaling from a structural viewpoint—what are we missing? The FEBS Journal 283(24):4424-4451.

68.

Casper Højgaard, Christian Kofoed, Roall Espersen, Kristoffer Enøe Johansson, Mara Villa, Martin Willemoës, Kresten Lindorff-Larsen, Kaare Teilum and Jakob R. Winther. (2016) A soluble, folded protein without charged amino acid residues Biochemistry 55(28):3949–3956.

69.

Elena Papaleo, Giorgio Saladino, Matteo Lambrughi, Kresten Lindorff-Larsen, Francesco Luigi Gervasio and Ruth Nussinov. (2016) The role of protein loops and linkers in conformational dynamics and allostery Chemical Reviews 116(11):6391-6423.

70.

Katrine Østergaard Bugge, Elena Papaleo, Gitte Wolfsberg Haxholm, Jonathan T.S. Hopper, Carol V. Robinson, Johan Gotthardt Olsen, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2016) A combined computational and structural model of the full-length human prolactin receptor Nature Communications 7.

71.

Kresten Lindorff-Larsen, Paul Maragakis, Stefano Piana and David E Shaw. (2016) Picosecond to Millisecond Structural Dynamics in Human Ubiquitin Journal of Physical Chemistry B 120(33):8313-8320.

72.

Kristoffer Enøe Johansson, Nicolai Tidemand Johansen, Signe Christensen, Scott Horowitz, James C. A. Bardwell, Johan Gotthardt Olsen, Martin Willemoës, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Wim Hamelryck and Jakob R. Winther. (2016) Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template Journal of Molecular Biology 428(21):4361-4377.

73.

Maher Mahmoud Kassem, Yong Wang, Wouter Krogh Boomsma and Kresten Lindorff-Larsen. (2016) Structure of the bacterial cytoskeleton protein bactofilin by NMR chemical shifts and sequence variation Biophysical Journal 110(11):2342-2348.

74.

Matteo Lambrughi, Luca De Gioia, Francesco Luigi Gervasio, Kresten Lindorff-Larsen, Ruth Nussinov, Chiara Urani, Maurizio Bruschi and Elena Papaleo. (2016) DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions Nucleic Acids Research 44(19):9096-9109.

75.

Nicholas Peter Schafer, Ha H. Truong, Daniel E. Otzen, Kresten Lindorff-Larsen and Peter G. Wolynes. (2016) Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease Proceedings of the National Academy of Sciences of the United States of America 113(8):2098-2103.

76.

Pengfei Tian, Kresten Lindorff-Larsen, Wouter Krogh Boomsma, Mogens Hogh Jensen and Daniel Erik Otzen. (2016) A Monte Carlo study of the early steps of functional amyloid formation P L o S One 11(1).

77.

Richard T. Timms, Sam A. Menzies, Iva A. Tchasovnikarova, Lea Cecilie Christensen, James C. Williamson, Robin Antrobus, Gordon Dougan, Lars Ellgaard and Paul J. Lehner. (2016) Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens Nature Communications 7.

78.

Wouter Krogh Boomsma, Sofie Vincents Nielsen, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen and Lars Ellgaard. (2016) Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases PeerJ 4.

79.

Yong Wang, Elena Papaleo and Kresten Lindorff-Larsen. (2016) Mapping transiently formed and sparsely populated conformations on a complex energy landscape eLife 5.

2015

80.

Fernando Martin-García, Elena Papaleo, Paulino Gomez-Puertas, Wouter Krogh Boomsma and Kresten Lindorff-Larsen. (2015) Comparing molecular dynamics force fields in the essential subspace PLoS ONE 10(3).

81.

Katrine Østergaard Bugge, Helena Steinocher, Andrew J. Brooks, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2015) Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy Analytical Chemistry 87(18):9126–9131.

82.

Lorenzo Sborgi, Abhinav Verma, Stefano Piana, Kresten Lindorff-Larsen, Michele Cerminara, Clara M. Santiveri, David E. Shaw, Eva De Alba and Victor Muñoz. (2015) Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations Journal of the American Chemical Society 137(20):6506-6516.

83.

Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Krogh Boomsma and Kresten Lindorff-Larsen. (2015) ENCORE: Software for Quantitative Ensemble Comparison PloS Computational Biology 11(10).

84.

Pengfei Tian, Wouter Krogh Boomsma, Yong Wang, Daniel Erik Otzen, Mogens Høgh Jensen and Kresten Lindorff-Larsen. (2015) What does evolution tell us about the structure of a functional amyloid protein? Biophysical Journal 108:227a.

85.

Pengfei Tian, Wouter Krogh Boomsma, Yong Wang, Daniel Otzen, Mogens Høgh Jensen and Kresten Lindorff-Larsen. (2015) Structure of a functional amyloid protein subunit computed using sequence variation Journal of the American Chemical Society 137(1):22–25.

86.

Søs Grønbæk Mathiassen, Ida B. Larsen, Esben Guldahl Poulsen, Christian Toft Madsen, Elena Papaleo, Kresten Lindorff-Larsen, Birthe Brandt Kragelund, Michael Lund Nielsen, Franziska Kriegenburg and Rasmus Hartmann-Petersen. (2015) A two-step protein quality control pathway for a misfolded DJ-1 variant in fission yeast The Journal of Biological Chemistry 290(34):21141-21153.

2014

87.

Elena Papaleo, Ludovico Sutto, Francesco Luigi Gervasio and Kresten Lindorff-Larsen. (2014) Conformational changes and free energies in a Proline isomerase Journal of Chemical Theory and Computation 10(9):4169-4174.

88.

Gaetano Invernizzi, Matteo Tiberti, Matteo Lambrughi, Kresten Lindorff-Larsen and Elena Papaleo. (2014) Communication routes in ARID domains between distal residues in Helix 5 and the DNA-binding loops P L o S Computational Biology (Online) 10(9).

89.

Pengfei Tian, Sigurður Ægir Jónsson, Jesper Ferkinghoff-Borg, Sergei V . Krivov, Kresten Lindorff-Larsen, Anders Irbäck and Wouter Krogh Boomsma. (2014) Robust estimation of diffusion-optimized ensembles for enhanced sampling Journal of Chemical Theory and Computation 10(2):543–553.

90.

Simon Olsson, Beat Rolf Vögeli, Andrea Cavalli, Wouter Krogh Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen and Thomas Wim Hamelryck. (2014) Probabilistic determination of native state ensembles of proteins Journal of Chemical Theory and Computation 10(8):3484-3491.

91.

Wouter Krogh Boomsma, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen. (2014) Combining experiments and simulations using the maximum entropy principle PloS Computational Biology 10(2).

92.

Wouter Krogh Boomsma, Pengfei Tian, Jes Frellsen, Jesper Ferkinghoff-Borg, Thomas Wim Hamelryck, Kresten Lindorff-Larsen and Michele Vendruscolo. (2014) Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts Proceedings of the National Academy of Sciences of the United States of America 111(38):13852-13857.

2013

93.

Anders Steen Christensen, Troels Emtekær Linnet, Mikael Borg, Wouter Krogh Boomsma, Kresten Lindorff-Larsen, Thomas Wim Hamelryck and Jan Halborg Jensen. (2013) Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics PLoS ONE 8(12).

94.

Anders Steen Christensen, Troels Emtekær Linnet, Mikael Borg, Wouter Krogh Boomsma, Kresten Lindorff-Larsen, Thomas Wim Hamelryck and Jan Halborg Jensen. (2013) Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics PLoS ONE 8(12).

95.

Jens Munk, Lea Thøgersen, Lars Erik Uggerhøj, Reinhard Wimmer, Niels Frimodt-Møller, Kresten Lindorff-Larsen and Paul Robert Hansen. (2013) The Structure of the Central Side Chain is Crucial for Anoplin Hemolytic Activity False.

96.

Sandro Bottaro, Kresten Lindorff-Larsen and Robert B. Best. (2013) Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data Journal of Chemical Theory and Computation 9(12):5641-5652.

97.

Stefano Piana, Kresten Lindorff-Larsen and David E. Shaw. (2013) Atomic-level description of ubiquitin folding Proceedings of the National Academy of Sciences of the United States of America 110(15):5915-5920.

98.

Stefano Piana, Kresten Lindorff-Larsen and David E. Shaw. (2013) Atomistic description of the folding of a dimeric protein Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 117(42):12935-12942.

99.

Wouter Krogh Boomsma, Jes Frellsen, Tim Philipp Harder, Sandro Bottaro, Kristoffer Enøe Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Simon Olsson, Jan Valentin, Lubomir Dimitrov Antonov, Anders Steen Christensen, Mikael Borg, Jan Halborg Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg and Thomas Wim Hamelryck. (2013) PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure Journal of Computational Chemistry 34(19):1697-1705.

2012

100.

Elena Papaleo, Kresten Lindorff-Larsen and Luca De Gioia. (2012) Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation Physical Chemistry Chemical Physics 14:12515-12525.

101.

Esben G Poulsen, Cornelia Steinhauer, Michael Lees, Anne-Marie Lauridsen, Lars Ellgaard and Rasmus Hartmann-Petersen. (2012) HUWE1 and TRIP12 Collaborate in Degradation of Ubiquitin-Fusion Proteins and Misframed Ubiquitin P L o S One 7(11).

102.

Kresten Lindorff-Larsen, Nikola Trbovic, Paul Maragakis, Stefano Piana and David E Shaw. (2012) Structure and dynamics of an unfolded protein examined by molecular dynamics simulation Journal of the American Chemical Society 134(8):3787-3791.

103.

Kresten Lindorff-Larsen, Paul Maragakis, Stefano Piana, Michael P Eastwood, Ron O Dror and David E Shaw. (2012) Systematic validation of protein force fields against experimental data P L o S One 7(2).

104.

Stefano Piana, Kresten Lindorff-Larsen and David E. Shaw. (2012) Protein folding kinetics and thermodynamics from atomistic simulation Proceedings of the National Academy of Sciences of the United States of America 109(44):17845-17850.

105.

Stefano Piana, Kresten Lindorff-Larsen, Robert M Dirks, John K Salmon, Ron O Dror and David E Shaw. (2012) Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations P L o S One 7(6).

2011

106.

Stefano Piana, Krishnarjun Sarkar, Kresten Lindorff-Larsen, Minghao Guo, Martin Gruebele and David E Shaw. (2011) Computational design and experimental testing of the fastest-folding ß-sheet protein Journal of Molecular Biology 405(1):43-48.

107.

Kresten Lindorff-Larsen, Stefano Piana, Ron O Dror and David E Shaw. (2011) How fast-folding proteins fold Science (New York, N.Y.) 334(6055):517-20.

108.

Stefano Piana, Kresten Lindorff-Larsen and David E Shaw. (2011) How robust are protein folding simulations with respect to force field parameterization? Biophysical Journal (2011) 100(9):L47-L49.

2010

109.

Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror and David E Shaw. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins: Structure, Function, and Bioinformatics 78(8):1950-8.

110.

David E Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O Dror, Michael P Eastwood, Joseph A Bank, John M Jumper, John K Salmon, Yibing Shan and Willy Wriggers. (2010) Atomic-level characterization of the structural dynamics of proteins Science (New York, N.Y.) 330(6002):341-6.

111.

Morten ؠJensen, David W Borhani, Kresten Lindorff-Larsen, Paul Maragakis, Vishwanath Jogini, Michael P Eastwood, Ron O Dror and David E Shaw. (2010) Principles of conduction and hydrophobic gating in K+ channels Proceedings of the National Academy of Sciences of the United States of America 107(13):5833-8.

2009

112.

Willy Wriggers, Kate A. Stafford, Yibing Shan, Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror and David E. Shaw. (2009) Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations Journal of Chemical Theory and Computation 5(10):2595-2605.

113.

David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Doug Ierardi, John L. Klepeis, Jeffrey Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan and Brian Towles. (2009) Millisecond-scale molecular dynamics simulations on Anton False.

114.

John L Klepeis, Kresten Lindorff-Larsen, Ron O Dror and David E Shaw. (2009) Long-timescale molecular dynamics simulations of protein structure and function Current Opinion in Structural Biology 19(2):120-7.

115.

Kresten Lindorff-Larsen and Jesper Ferkinghoff-Borg. (2009) Similarity measures for protein ensembles PLoS ONE 4(1).

2008

116.

Anders B. Nørgaard, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen. (2008) Experimental parameterization of an energy function for the simulation of unfolded proteins Biophysical Journal 94(1):182-192.

117.

Paul Maragakis, Kresten Lindorff-Larsen, Michael P Eastwood, Ron O Dror, John L Klepeis, Isaiah T Arkin, Morten ؠJensen, Huafeng Xu, Nikola Trbovic, Richard A Friesner, Arthur G Palmer Iii and David E Shaw. (2008) Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 112(19):6155-6158.

2007

118.

Christian D Geierhaas, Adrian A Nickson, Kresten Lindorff-Larsen, Jane Clarke and Michele Vendruscolo. (2007) BPPred: a Web-based computational tool for predicting biophysical parameters of proteins Protein Science 16(1):125-34.

119.

Kristofer Modig, Vibeke W. Jürgensen, Kresten Lindorff-Larsen, Wolfgang Fieber, Henrik G Bohr and Flemming Martin Poulsen. (2007) Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis. FEBS Letters 581(25):4965-4971.

2006

120.

C. J. Francis, Kresten Lindorff-Larsen, R. B. Best and M. Bendruscolo. (2006) Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease Proteins - Structure Function and Bioinformatics 65(1):145-52.

121.

M. Louhivuori, R. Otten, Kresten Lindorff-Larsen and A. Annila. (2006) Conformational fluctuations affect protein alignment in dilute liquid crystal media. Journal of the American Chemical Society 128(13):4371-4376.

122.

R. B. Best, Kresten Lindorff-Larsen, M. A. DePristo and M. VEndruscolo. (2006) Relation between native ensembles and experimental structures of proteins. Proceedings of the National Academy of Science of the United States of America 103(29):10901-6.

123.

Vidya Chandran, Elliott J Stollar, Kresten Lindorff-Larsen, Jeffrey F Harper, Walter J Chazin, Christopher M Dobson, Ben F Luisi and John Christodoulou. (2006) Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition Journal of Molecular Biology 357(2):400-10.

2005

124.

Emanuele Paci, K. Lindorff-Larsen, Christopher M. Dobson, Martin Karplus and Michele Vendruscolo. (2005) Transition State Contact Orders Correlate with Protein Folding Rates Journal of Molecular Biology 352(3):495-500.

125.

Kresten Lindorff-Larsen, Robert B. Best and Michele Vendruscolo. (2005) Interpreting Dynamically-Averaged Scalar Couplings in Proteins Journal of Biomolecular NMR 32(4):273-280.

126.

Kresten Lindorff-Larsen, Robert B. Best, M. A. DePristo, C. M. Dobson and Michele Vendruscolo. (2005) Simultaneous determination of protein structure and dynamics Nature 433(7022):128-132.

127.

M. M. Dedmon, K. Lindorff-Larsen, J. Christodoulou, Michele Vendruscolo and C. M. Dobson. (2005) Mapping Long-Range Interactions in a-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations Journal of the American Chemical Society 127(2):476-477.

128.

S. Kristjansdottir, Kresten Lindorff-Larsen, W. Fieber, Christopher M. Dobson, Michele Vendruscolo and Flemming M. Poulsen. (2005) Formation of Native and Non-native Interactions in Ensembles of Denatured ACBP Molecules from Paramagnetic Relaxation Enhancement Studies Journal of Molecular Biology 347(5):1053-1062.

2004

129.

Emanuele Paci, Claire T Friel, Kresten Lindorff-Larsen, Sheena E Radford, Martin Karplus and Michele Vendruscolo. (2004) Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints Proteins: Structure, Function, and Bioinformatics 54(3):513-25.

130.

Kresten Lindorff-Larsen, Michele Vendruscolo, Emanuele Paci and Christopher M Dobson. (2004) Transition states for protein folding have native topologies despite high structural variability Nature Structural and Molecular Biology 11(5):443-9.

131.

Kresten Lindorff-Larsen, Sigridur Kristjansdottir, Kaare Teilum, Wolfgang Fieber, Christopher M Dobson, Flemming Martin Poulsen and Michele Vendruscolo. (2004) Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein Journal of the American Chemical Society 126(10):3291-3219.

2003

132.

Caroline F Wright, Kresten Lindorff-Larsen, Lucy G Randles and Jane Clarke. (2003) Parallel protein-unfolding pathways revealed and mapped Nature Structural and Molecular Biology 10(8):658-62.

133.

Kresten Lindorff-Larsen, Emanuele Paci, Luis Serrano, Christopher M Dobson and Michele Vendruscolo. (2003) Calculation of mutational free energy changes in transition states for protein folding Biophysical Journal 85(2):1207-14.

2001

134.

Kresten Lindorff-Larsen and Jakob R. Winther. (2001) Surprisingly high stability of barley lipid transfer protein, LTP1, towards denaturant, heat and proteases FEBS Letters 488(3):145-148.

135.

Kresten Lindorff-Larsen, Mathilde H. Lerche, Flemming Martin Poulsen, Peter Roepstorff and Jakob R. Winther. (2001) Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification Journal of Biological Chemistry 276(36):33547-53.

2000

136.

Kresten Lindorff-Larsen and Jakob R. Winther. (2000) Thiol alkylation below neutral pH Analytical Biochemistry 286(2):308-10.

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