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Kresten Lindorff-Larsen - Publications

Affiliations: 
Biology University of Copenhagen, København, Denmark 
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128 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
2023 Oxenfarth A, Kümmerer F, Bottaro S, Schnieders R, Pinter G, Jonker HRA, Fürtig B, Richter C, Blackledge M, Lindorff-Larsen K, Schwalbe H. Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop. Journal of the American Chemical Society. PMID 37479220 DOI: 10.1021/jacs.3c03578  0.762
2023 Cagiada M, Bottaro S, Lindemose S, Schenstrøm SM, Stein A, Hartmann-Petersen R, Lindorff-Larsen K. Discovering functionally important sites in proteins. Nature Communications. 14: 4175. PMID 37443362 DOI: 10.1038/s41467-023-39909-0  0.668
2023 Pesce F, Lindorff-Larsen K. Combining Experiments and Simulations to Examine the Temperature-Dependent Behavior of a Disordered Protein. The Journal of Physical Chemistry. B. PMID 37433228 DOI: 10.1021/acs.jpcb.3c01862  0.375
2023 Kümmerer F, Orioli S, Lindorff-Larsen K. Fitting Force Field Parameters to NMR Relaxation Data. Journal of Chemical Theory and Computation. 19: 3741-3751. PMID 37276045 DOI: 10.1021/acs.jctc.3c00174  0.385
2023 Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. Biorxiv : the Preprint Server For Biology. PMID 37205542 DOI: 10.1101/2023.05.02.538537  0.428
2023 González-Delgado J, Sagar A, Zanon C, Lindorff-Larsen K, Bernadó P, Neuvial P, Cortés J. WASCO: A Wasserstein-based statistical tool to compare conformational ensembles of intrinsically disordered proteins. Journal of Molecular Biology. 168053. PMID 36934808 DOI: 10.1016/j.jmb.2023.168053  0.405
2023 Thomasen FE, Cuneo MJ, Mittag T, Lindorff-Larsen K. Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations. Elife. 12. PMID 36856266 DOI: 10.7554/eLife.84147  0.38
2023 Montepietra D, Tesei G, Martins JOM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries. Biorxiv : the Preprint Server For Biology. PMID 36789411 DOI: 10.1101/2023.01.27.525885  0.368
2022 Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, ... ... Lindorff-Larsen K, et al. A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology. PMID 36344848 DOI: 10.1038/s41594-022-00849-w  0.303
2022 Thomasen FE, Pesce F, Roesgaard MA, Tesei G, Lindorff-Larsen K. Improving Martini 3 for Disordered and Multidomain Proteins. Journal of Chemical Theory and Computation. 18: 2033-2041. PMID 35377637 DOI: 10.1021/acs.jctc.1c01042  0.347
2022 Thomasen FE, Lindorff-Larsen K. Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochemical Society Transactions. 50: 541-554. PMID 35129612 DOI: 10.1042/BST20210499  0.318
2021 Tesei G, Schulze TK, Crehuet R, Lindorff-Larsen K. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34716273 DOI: 10.1073/pnas.2111696118  0.334
2021 Pesce F, Lindorff-Larsen K. Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data. Biophysical Journal. 120: 5124-5135. PMID 34627764 DOI: 10.1016/j.bpj.2021.10.003  0.321
2021 Jephthah S, Pesce F, Lindorff-Larsen K, Skepö M. Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. Journal of Chemical Theory and Computation. PMID 34524800 DOI: 10.1021/acs.jctc.1c00408  0.412
2021 Lindorff-Larsen K, Kragelund BB. On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins. Journal of Molecular Biology. 167196. PMID 34390736 DOI: 10.1016/j.jmb.2021.167196  0.323
2021 Kümmerer F, Orioli S, Harding-Larsen D, Hoffmann F, Gavrilov Y, Teilum K, Lindorff-Larsen K. Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations. Journal of Chemical Theory and Computation. 17: 5262-5275. PMID 34291646 DOI: 10.1021/acs.jctc.0c01338  0.44
2021 Kassem N, Araya-Secchi R, Bugge K, Barclay A, Steinocher H, Khondker A, Wang Y, Lenard AJ, Bürck J, Sahin C, Ulrich AS, Landreh M, Pedersen MC, Rheinstädter MC, Pedersen PA, ... Lindorff-Larsen K, et al. Order and disorder-An integrative structure of the full-length human growth hormone receptor. Science Advances. 7. PMID 34193419 DOI: 10.1126/sciadv.abh3805  0.308
2021 Kassem N, Araya-Secchi R, Bugge K, Barclay A, Steinocher H, Khondker A, Wang Y, Lenard AJ, Bürck J, Sahin C, Ulrich AS, Landreh M, Pedersen MC, Rheinstädter MC, Pedersen PA, ... Lindorff-Larsen K, et al. Order and disorder-An integrative structure of the full-length human growth hormone receptor. Science Advances. 7. PMID 34193419 DOI: 10.1126/sciadv.abh3805  0.308
2021 Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. Journal of the American Chemical Society. 143: 8333-8343. PMID 34039006 DOI: 10.1021/jacs.1c01094  0.815
2021 Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. Journal of the American Chemical Society. 143: 8333-8343. PMID 34039006 DOI: 10.1021/jacs.1c01094  0.815
2021 Ahmed MC, Skaanning LK, Jussupow A, Newcombe EA, Kragelund BB, Camilloni C, Langkilde AE, Lindorff-Larsen K. Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods. Frontiers in Molecular Biosciences. 8: 654333. PMID 33968988 DOI: 10.3389/fmolb.2021.654333  0.436
2021 Ahmed MC, Skaanning LK, Jussupow A, Newcombe EA, Kragelund BB, Camilloni C, Langkilde AE, Lindorff-Larsen K. Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods. Frontiers in Molecular Biosciences. 8: 654333. PMID 33968988 DOI: 10.3389/fmolb.2021.654333  0.436
2021 Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K. DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. Plos Computational Biology. 17: e1008551. PMID 33481784 DOI: 10.1371/journal.pcbi.1008551  0.347
2020 Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K. Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations. Elife. 9. PMID 32729831 DOI: 10.7554/Elife.56518  0.745
2020 Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K. Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations. Elife. 9. PMID 32729831 DOI: 10.7554/Elife.56518  0.745
2020 Bottaro S, Nichols PJ, Vögeli B, Parrinello M, Lindorff-Larsen K. Integrating NMR and simulations reveals motions in the UUCG tetraloop. Nucleic Acids Research. PMID 32427326 DOI: 10.1093/Nar/Gkaa399  0.81
2020 Bottaro S, Nichols PJ, Vögeli B, Parrinello M, Lindorff-Larsen K. Integrating NMR and simulations reveals motions in the UUCG tetraloop. Nucleic Acids Research. PMID 32427326 DOI: 10.1093/Nar/Gkaa399  0.81
2020 Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. Plos Computational Biology. 16: e1007870. PMID 32339173 DOI: 10.1371/Journal.Pcbi.1007870  0.727
2020 Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. Plos Computational Biology. 16: e1007870. PMID 32339173 DOI: 10.1371/Journal.Pcbi.1007870  0.727
2020 Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. Progress in Molecular Biology and Translational Science. 170: 123-176. PMID 32145944 DOI: 10.1016/Bs.Pmbts.2019.12.006  0.755
2020 Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. Progress in Molecular Biology and Translational Science. 170: 123-176. PMID 32145944 DOI: 10.1016/Bs.Pmbts.2019.12.006  0.755
2020 Bottaro S, Bengtsen T, Lindorff-Larsen K. Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach. Methods in Molecular Biology (Clifton, N.J.). 2112: 219-240. PMID 32006288 DOI: 10.1007/978-1-0716-0270-6_15  0.768
2020 Bottaro S, Bengtsen T, Lindorff-Larsen K. Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach. Methods in Molecular Biology (Clifton, N.J.). 2112: 219-240. PMID 32006288 DOI: 10.1007/978-1-0716-0270-6_15  0.768
2020 Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K. Author response: Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations Elife. DOI: 10.7554/Elife.56518.Sa2  0.745
2020 Lindorff-Larsen K. Combining Biophysical Experiments and Biomolecular Simulations Biophysical Journal. 118: 321a. DOI: 10.1016/j.bpj.2019.11.1804  0.349
2019 Bonomi M, Bussi G, Camilloni C, Tribello GA, Banáš P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen H, ... ... Lindorff-Larsen K, et al. Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods. 16: 670-673. PMID 31363226 DOI: 10.1038/S41592-019-0506-8  0.799
2019 Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Sponer J, Bussi G. Fitting corrections to an RNA force field using experimental data. Journal of Chemical Theory and Computation. PMID 31050905 DOI: 10.1021/Acs.Jctc.9B00206  0.773
2019 Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Sponer J, Bussi G. Fitting corrections to an RNA force field using experimental data. Journal of Chemical Theory and Computation. PMID 31050905 DOI: 10.1021/Acs.Jctc.9B00206  0.773
2018 Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K. Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories. Rna (New York, N.Y.). PMID 30420522 DOI: 10.1261/Rna.067678.118  0.799
2018 Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K. Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories. Rna (New York, N.Y.). PMID 30420522 DOI: 10.1261/Rna.067678.118  0.799
2018 Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. The Journal of Physical Chemistry. B. PMID 30141937 DOI: 10.1021/Acs.Jpcb.8B06335  0.39
2018 Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. The Journal of Physical Chemistry. B. PMID 30141937 DOI: 10.1021/Acs.Jpcb.8B06335  0.39
2018 Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K. Frequency adaptive metadynamics for the calculation of rare-event kinetics. The Journal of Chemical Physics. 149: 072309. PMID 30134721 DOI: 10.1063/1.5024679  0.478
2018 Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K. Frequency adaptive metadynamics for the calculation of rare-event kinetics. The Journal of Chemical Physics. 149: 072309. PMID 30134721 DOI: 10.1063/1.5024679  0.478
2018 Bottaro S, Lindorff-Larsen K. Biophysical experiments and biomolecular simulations: A perfect match? Science (New York, N.Y.). 361: 355-360. PMID 30049874 DOI: 10.1126/Science.Aat4010  0.738
2018 Bottaro S, Lindorff-Larsen K. Biophysical experiments and biomolecular simulations: A perfect match? Science (New York, N.Y.). 361: 355-360. PMID 30049874 DOI: 10.1126/Science.Aat4010  0.738
2018 Papaleo E, Camilloni C, Teilum K, Vendruscolo M, Lindorff-Larsen K. Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs. Peerj. 6: e5125. PMID 30013831 DOI: 10.7717/Peerj.5125  0.439
2018 Ahmed MC, Papaleo E, Lindorff-Larsen K. How well do force fields capture the strength of salt bridges in proteins? Peerj. 6: e4967. PMID 29910983 DOI: 10.7717/peerj.4967  0.438
2018 Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Science Advances. 4: eaar8521. PMID 29795785 DOI: 10.1126/Sciadv.Aar8521  0.82
2018 Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Science Advances. 4: eaar8521. PMID 29795785 DOI: 10.1126/Sciadv.Aar8521  0.82
2018 Best RB, Lindorff-Larsen K. Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level. Current Opinion in Structural Biology. 49: iv-v. PMID 29685339 DOI: 10.1016/j.sbi.2018.04.002  0.335
2018 Best RB, Lindorff-Larsen K. Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level. Current Opinion in Structural Biology. 49: iv-v. PMID 29685339 DOI: 10.1016/j.sbi.2018.04.002  0.335
2018 Henriques J, Arleth L, Lindorff-Larsen K, Skepö M. On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations. Journal of Molecular Biology. 430: 2521-2539. PMID 29548755 DOI: 10.1016/j.jmb.2018.03.002  0.369
2018 Henriques J, Arleth L, Lindorff-Larsen K, Skepö M. On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations. Journal of Molecular Biology. 430: 2521-2539. PMID 29548755 DOI: 10.1016/j.jmb.2018.03.002  0.369
2018 Truelsen SF, Wang Y, Lindorff-Larsen K, Hélix-Nielsen C. Towards Biomimetic Phosphate Recovery: Molecular Dynamics Simulations of Phosphate Binding Proteins Biophysical Journal. 114: 57a. DOI: 10.1016/J.BPJ.2017.11.364  0.347
2018 Bengtsen T, Holm VL, Midtgaard SR, Arleth L, Lindorff-Larsen K. A Combined Simulation and SAXS Study of the Dynamics of Lipid Nanodiscs Biophysical Journal. 114: 559a. DOI: 10.1016/j.bpj.2017.11.3055  0.35
2017 Nygaard M, Kragelund BB, Papaleo E, Lindorff-Larsen K. An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophysical Journal. 113: 550-557. PMID 28793210 DOI: 10.1016/j.bpj.2017.06.042  0.384
2017 Nygaard M, Kragelund BB, Papaleo E, Lindorff-Larsen K. An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophysical Journal. 113: 550-557. PMID 28793210 DOI: 10.1016/j.bpj.2017.06.042  0.384
2017 Bottaro S, Lindorff-Larsen K. Mapping the Universe of RNA Tetraloop Folds. Biophysical Journal. 113: 257-267. PMID 28673616 DOI: 10.1016/J.Bpj.2017.06.011  0.68
2017 Bottaro S, Lindorff-Larsen K. Mapping the Universe of RNA Tetraloop Folds. Biophysical Journal. 113: 257-267. PMID 28673616 DOI: 10.1016/J.Bpj.2017.06.011  0.68
2017 Choy MS, Li Y, Machado LE, Kunze MB, Connors CR, Wei X, Lindorff-Larsen K, Page R, Peti W. Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery. Molecular Cell. 65: 644-658.e5. PMID 28212750 DOI: 10.1016/J.Molcel.2017.01.014  0.314
2017 Bottaro S, Lindorff-Larsen K, Best RB. Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data. Journal of Chemical Theory and Computation. 13: 392. PMID 27990814 DOI: 10.1021/Acs.Jctc.6B01188  0.696
2017 Bottaro S, Lindorff-Larsen K, Best RB. Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data. Journal of Chemical Theory and Computation. 13: 392. PMID 27990814 DOI: 10.1021/Acs.Jctc.6B01188  0.696
2016 Wang Y, Papaleo E, Lindorff-Larsen K. Mapping transiently formed and sparsely populated conformations on a complex energy landscape. Elife. 5. PMID 27552057 DOI: 10.7554/eLife.17505  0.419
2016 Kassem MM, Wang Y, Boomsma W, Lindorff-Larsen K. Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation. Biophysical Journal. 110: 2342-2348. PMID 27276252 DOI: 10.1016/J.Bpj.2016.04.039  0.303
2016 Lindorff-Larsen K, Maragakis P, Piana S, Shaw DE. Picosecond to Millisecond Structural Dynamics in Human Ubiquitin. The Journal of Physical Chemistry. B. PMID 27082121 DOI: 10.1021/acs.jpcb.6b02024  0.421
2016 Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chemical Reviews. 116: 6391-423. PMID 26889708 DOI: 10.1021/Acs.Chemrev.5B00623  0.325
2015 Tiberti M, Papaleo E, Bengtsen T, Boomsma W, Lindorff-Larsen K. ENCORE: Software for Quantitative Ensemble Comparison Plos Computational Biology. 11. PMID 26505632 DOI: 10.1371/Journal.Pcbi.1004415  0.493
2015 Tiberti M, Papaleo E, Bengtsen T, Boomsma W, Lindorff-Larsen K. ENCORE: Software for Quantitative Ensemble Comparison Plos Computational Biology. 11. PMID 26505632 DOI: 10.1371/Journal.Pcbi.1004415  0.493
2015 Sborgi L, Verma A, Piana S, Lindorff-Larsen K, Cerminara M, Santiveri CM, Shaw DE, de Alba E, Muñoz V. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations. Journal of the American Chemical Society. 137: 6506-16. PMID 25924808 DOI: 10.1021/Jacs.5B02324  0.414
2015 Sborgi L, Verma A, Piana S, Lindorff-Larsen K, Cerminara M, Santiveri CM, Shaw DE, de Alba E, Muñoz V. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations. Journal of the American Chemical Society. 137: 6506-16. PMID 25924808 DOI: 10.1021/Jacs.5B02324  0.414
2015 Martín-García F, Papaleo E, Gomez-Puertas P, Boomsma W, Lindorff-Larsen K. Comparing molecular dynamics force fields in the essential subspace. Plos One. 10: e0121114. PMID 25811178 DOI: 10.1371/Journal.Pone.0121114  0.443
2015 Martín-García F, Papaleo E, Gomez-Puertas P, Boomsma W, Lindorff-Larsen K. Comparing molecular dynamics force fields in the essential subspace. Plos One. 10: e0121114. PMID 25811178 DOI: 10.1371/Journal.Pone.0121114  0.443
2015 Lindorff-Larsen K. Watching Conformational Changes in Proteins by Molecular Dynamics Simulations Biophysical Journal. 108: 380a. DOI: 10.1016/J.BPJ.2014.11.2085  0.413
2014 Papaleo E, Sutto L, Gervasio FL, Lindorff-Larsen K. Conformational Changes and Free Energies in a Proline Isomerase. Journal of Chemical Theory and Computation. 10: 4169-74. PMID 26588555 DOI: 10.1021/ct500536r  0.379
2014 Papaleo E, Sutto L, Gervasio FL, Lindorff-Larsen K. Conformational Changes and Free Energies in a Proline Isomerase. Journal of Chemical Theory and Computation. 10: 4169-74. PMID 26588555 DOI: 10.1021/ct500536r  0.379
2014 Boomsma W, Tian P, Frellsen J, Ferkinghoff-Borg J, Hamelryck T, Lindorff-Larsen K, Vendruscolo M. 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: 13852-7. PMID 25192938 DOI: 10.1073/Pnas.1404948111  0.447
2014 Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K. Combining experiments and simulations using the maximum entropy principle. Plos Computational Biology. 10: e1003406. PMID 24586124 DOI: 10.1371/Journal.Pcbi.1003406  0.372
2013 Bottaro S, Lindorff-Larsen K, Best RB. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data. Journal of Chemical Theory and Computation. 9: 5641-5652. PMID 24748852 DOI: 10.1021/Ct400730N  0.737
2013 Bottaro S, Lindorff-Larsen K, Best RB. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data. Journal of Chemical Theory and Computation. 9: 5641-5652. PMID 24748852 DOI: 10.1021/Ct400730N  0.737
2013 Piana S, Lindorff-Larsen K, Shaw DE. Atomistic description of the folding of a dimeric protein. The Journal of Physical Chemistry. B. 117: 12935-42. PMID 23882999 DOI: 10.1021/Jp4020993  0.357
2013 Boomsma W, Frellsen J, Harder T, Bottaro S, Johansson KE, Tian P, Stovgaard K, Andreetta C, Olsson S, Valentin JB, Antonov LD, Christensen AS, Borg M, Jensen JH, Lindorff-Larsen K, et al. PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure. Journal of Computational Chemistry. 34: 1697-705. PMID 23619610 DOI: 10.1002/Jcc.23292  0.74
2013 Boomsma W, Frellsen J, Harder T, Bottaro S, Johansson KE, Tian P, Stovgaard K, Andreetta C, Olsson S, Valentin JB, Antonov LD, Christensen AS, Borg M, Jensen JH, Lindorff-Larsen K, et al. PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure. Journal of Computational Chemistry. 34: 1697-705. PMID 23619610 DOI: 10.1002/Jcc.23292  0.74
2013 Piana S, Lindorff-Larsen K, Shaw DE. Atomic-level description of ubiquitin folding. Proceedings of the National Academy of Sciences of the United States of America. 110: 5915-20. PMID 23503848 DOI: 10.1073/Pnas.1218321110  0.382
2013 Boomsma W, Lindorff-Larsen K. A sticky cage can slow down folding. Biophysical Journal. 104: 964-5. PMID 23473477 DOI: 10.1016/J.Bpj.2013.01.036  0.368
2012 Piana S, Lindorff-Larsen K, Shaw DE. Protein folding kinetics and thermodynamics from atomistic simulation. Proceedings of the National Academy of Sciences of the United States of America. 109: 17845-50. PMID 22822217 DOI: 10.1073/Pnas.1201811109  0.437
2012 Piana S, Lindorff-Larsen K, Shaw DE. Protein folding kinetics and thermodynamics from atomistic simulation. Proceedings of the National Academy of Sciences of the United States of America. 109: 17845-50. PMID 22822217 DOI: 10.1073/Pnas.1201811109  0.437
2012 Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE. Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. Plos One. 7: e39918. PMID 22768169 DOI: 10.1371/Journal.Pone.0039918  0.41
2012 Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE. Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. Plos One. 7: e39918. PMID 22768169 DOI: 10.1371/Journal.Pone.0039918  0.41
2012 Papaleo E, Lindorff-Larsen K, De Gioia L. Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation. Physical Chemistry Chemical Physics : Pccp. 14: 12515-25. PMID 22706570 DOI: 10.1039/c2cp41224a  0.356
2012 Papaleo E, Lindorff-Larsen K, De Gioia L. Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation. Physical Chemistry Chemical Physics : Pccp. 14: 12515-25. PMID 22706570 DOI: 10.1039/c2cp41224a  0.356
2012 Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE. Systematic validation of protein force fields against experimental data. Plos One. 7: e32131. PMID 22384157 DOI: 10.1371/journal.pone.0032131  0.465
2012 Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE. Systematic validation of protein force fields against experimental data. Plos One. 7: e32131. PMID 22384157 DOI: 10.1371/journal.pone.0032131  0.465
2012 Lindorff-Larsen K, Trbovic N, Maragakis P, Piana S, Shaw DE. Structure and dynamics of an unfolded protein examined by molecular dynamics simulation Journal of the American Chemical Society. 134: 3787-3791. PMID 22339051 DOI: 10.1021/Ja209931W  0.467
2012 Lindorff-Larsen K, Trbovic N, Maragakis P, Piana S, Shaw DE. Structure and dynamics of an unfolded protein examined by molecular dynamics simulation Journal of the American Chemical Society. 134: 3787-3791. PMID 22339051 DOI: 10.1021/Ja209931W  0.467
2011 Lindorff-Larsen K, Piana S, Dror RO, Shaw DE. How fast-folding proteins fold. Science (New York, N.Y.). 334: 517-20. PMID 22034434 DOI: 10.1126/science.1208351  0.395
2011 Lindorff-Larsen K, Piana S, Dror RO, Shaw DE. How fast-folding proteins fold. Science (New York, N.Y.). 334: 517-20. PMID 22034434 DOI: 10.1126/science.1208351  0.395
2011 Piana S, Lindorff-Larsen K, Shaw DE. How robust are protein folding simulations with respect to force field parameterization? Biophysical Journal. 100: L47-L49. PMID 21539772 DOI: 10.1016/j.bpj.2011.03.051  0.438
2011 Piana S, Lindorff-Larsen K, Shaw DE. How robust are protein folding simulations with respect to force field parameterization? Biophysical Journal. 100: L47-L49. PMID 21539772 DOI: 10.1016/j.bpj.2011.03.051  0.438
2011 Piana S, Sarkar K, Lindorff-Larsen K, Guo M, Gruebele M, Shaw DE. Computational design and experimental testing of the fastest-folding β-sheet protein. Journal of Molecular Biology. 405: 43-8. PMID 20974152 DOI: 10.1016/J.Jmb.2010.10.023  0.385
2011 Piana S, Sarkar K, Lindorff-Larsen K, Guo M, Gruebele M, Shaw DE. Computational design and experimental testing of the fastest-folding β-sheet protein. Journal of Molecular Biology. 405: 43-8. PMID 20974152 DOI: 10.1016/J.Jmb.2010.10.023  0.385
2010 Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-level characterization of the structural dynamics of proteins. Science (New York, N.Y.). 330: 341-6. PMID 20947758 DOI: 10.1126/Science.1187409  0.415
2010 Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-level characterization of the structural dynamics of proteins. Science (New York, N.Y.). 330: 341-6. PMID 20947758 DOI: 10.1126/Science.1187409  0.415
2010 Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 78: 1950-8. PMID 20408171 DOI: 10.1002/prot.22711  0.392
2010 Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 78: 1950-8. PMID 20408171 DOI: 10.1002/prot.22711  0.392
2009 Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 5: 2595-605. PMID 26631775 DOI: 10.1021/Ct900229U  0.402
2009 Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 5: 2595-605. PMID 26631775 DOI: 10.1021/Ct900229U  0.402
2009 Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology. 19: 120-7. PMID 19361980 DOI: 10.1016/j.sbi.2009.03.004  0.461
2009 Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology. 19: 120-7. PMID 19361980 DOI: 10.1016/j.sbi.2009.03.004  0.461
2009 Lindorff-Larsen K, Ferkinghoff-Borg J. Similarity measures for protein ensembles. Plos One. 4: e4203. PMID 19145244 DOI: 10.1371/journal.pone.0004203  0.389
2009 Lindorff-Larsen K, Ferkinghoff-Borg J. Similarity measures for protein ensembles. Plos One. 4: e4203. PMID 19145244 DOI: 10.1371/journal.pone.0004203  0.389
2009 Shaw DE, Dror RO, Salmon JK, Grossman JP, MacKenzie KM, Bank JA, Young C, Deneroff MM, Batson B, Bowers KJ, Chow E, Eastwood MP, Ierardi DJ, Klepeis JL, Kuskin JS, ... ... Lindorff-Larsen K, et al. Millisecond-scale molecular dynamics simulations on Anton Proceedings of the Conference On High Performance Computing Networking, Storage and Analysis, Sc '09. DOI: 10.1145/1654059.1654099  0.363
2009 Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. Automated event detection and activity monitoring in long molecular dynamics simulations Journal of Chemical Theory and Computation. 5: 2595-2605. DOI: 10.1021/ct900229u  0.313
2009 Piana-Agostinetti S, Lindorff-Larsen K, Maragakis P, Eastwood MP, Dror RO, Shaw DE. Improving Molecular Mechanics Force Fields By Comparison Of Microsecond Simulations With Nmr Experiments Biophysical Journal. 96: 406a. DOI: 10.1016/J.Bpj.2008.12.2066  0.48
2009 Wriggers W, Stafford KA, Shan Y, Piana-Agostinetti S, Maragakis P, Lindorff-Larsen K, Miller PJ, Eastwood MP, Dror RO, Shaw DE. Automated Event Detection and Activity Monitoring in Long Time-Scale Molecular Dynamics Biophysical Journal. 96: 364a-365a. DOI: 10.1016/J.Bpj.2008.12.1962  0.379
2008 Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Iii AG, Shaw DE. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8. PMID 18311962 DOI: 10.1021/Jp077018H  0.471
2008 Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Iii AG, Shaw DE. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8. PMID 18311962 DOI: 10.1021/Jp077018H  0.471
2008 Norgaard AB, Ferkinghoff-Borg J, Lindorff-Larsen K. Experimental parameterization of an energy function for the simulation of unfolded proteins. Biophysical Journal. 94: 182-92. PMID 17827232 DOI: 10.1529/biophysj.107.108241  0.382
2008 Norgaard AB, Ferkinghoff-Borg J, Lindorff-Larsen K. Experimental parameterization of an energy function for the simulation of unfolded proteins. Biophysical Journal. 94: 182-92. PMID 17827232 DOI: 10.1529/biophysj.107.108241  0.382
2006 Francis CJ, Lindorff-Larsen K, Best RB, Vendruscolo M. Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease. Proteins. 65: 145-52. PMID 16862593 DOI: 10.1002/Prot.21077  0.358
2006 Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M. Relation between native ensembles and experimental structures of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 10901-6. PMID 16829580 DOI: 10.1073/Pnas.0511156103  0.324
2006 Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M. Relation between native ensembles and experimental structures of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 10901-6. PMID 16829580 DOI: 10.1073/Pnas.0511156103  0.324
2006 Louhivuori M, Otten R, Lindorff-Larsen K, Annila A. Conformational fluctuations affect protein alignment in dilute liquid crystal media Journal of the American Chemical Society. 128: 4371-4376. PMID 16569014 DOI: 10.1021/ja0576334  0.309
2006 Louhivuori M, Otten R, Lindorff-Larsen K, Annila A. Conformational fluctuations affect protein alignment in dilute liquid crystal media Journal of the American Chemical Society. 128: 4371-4376. PMID 16569014 DOI: 10.1021/ja0576334  0.309
2006 Lindorff-Larsen K, Best RB, Vendruscolo M. Interpreting dynamically-averaged scalar couplings in proteins. Journal of Biomolecular Nmr. 32: 273-80. PMID 16211481 DOI: 10.1007/S10858-005-8873-0  0.324
2005 Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M. Simultaneous determination of protein structure and dynamics. Nature. 433: 128-32. PMID 15650731 DOI: 10.1038/Nature03199  0.393
2004 Lindorff-Larsen K, Kristjansdottir S, Teilum K, Fieber W, Dobson CM, Poulsen FM, Vendruscolo M. 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: 3291-9. PMID 15012160 DOI: 10.1021/Ja039250G  0.334
2004 Lindorff-Larsen K, Paci E, Serrano L, Dobson CM, Vendruscolo M. Calculation of mutational free energy changes in transition states for protein folding. Biophysical Journal. 85: 1207-14. PMID 12885664 DOI: 10.1016/S0006-3495(03)74556-1  0.305
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