Kresten Lindorff-Larsen

2016

Structure of the bacterial cytoskeleton protein bactofilin by NMR chemical shifts and sequence variation

Kassem, M. M., Wang, Y., Boomsma, W. K. & Lindorff-Larsen, K., 7 Jun 2016, In: Biophysical Journal. 110, 11, p. 2342-2348 7 p.

Research output: Contribution to journal › Journal article › Research › peer-review

9 Citations (Scopus)

The role of protein loops and linkers in conformational dynamics and allostery

Papaleo, E., Saladino, G., Lambrughi, M., Lindorff-Larsen, K., Gervasio, F. L. & Nussinov, R., 8 Jun 2016, In: Chemical Reviews. 116, 11, p. 6391-6423 33 p.

Research output: Contribution to journal › Review › peer-review

159 Citations (Scopus)

Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease

Schafer, N. P., Truong, H. H., Otzen, D. E., Lindorff-Larsen, K. & Wolynes, P. G., 23 Feb 2016, In: Proceedings of the National Academy of Sciences of the United States of America. 113, 8, p. 2098-2103 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

10 Citations (Scopus)

Understanding single-pass transmembrane receptor signaling from a structural viewpoint—what are we missing?

Bugge, K. Ø., Lindorff-Larsen, K. & Kragelund, B. B., 1 Dec 2016, In: The FEBS Journal. 283, 24, p. 4424-4451 28 p.

Research output: Contribution to journal › Review › peer-review

21 Citations (Scopus)

72 Downloads (Pure)

2015

A two-step protein quality control pathway for a misfolded DJ-1 variant in fission yeast

Mathiassen, S. G., Larsen, I. B., Poulsen, E. G., Madsen, C. T., Papaleo, E., Lindorff-Larsen, K., Kragelund, B. B., Nielsen, M. L., Kriegenburg, F. & Hartmann-Petersen, R., 21 Aug 2015, In: The Journal of Biological Chemistry. 290, 34, p. 21141-21153 13 p.

Research output: Contribution to journal › Journal article › Research › peer-review

15 Citations (Scopus)

Comparing molecular dynamics force fields in the essential subspace

Martin-García, F., Papaleo, E., Gomez-Puertas, P., Boomsma, W. K. & Lindorff-Larsen, K., 26 Mar 2015, In: PLoS ONE. 10, 3, 16 p., e0121114.

Research output: Contribution to journal › Journal article › Research › peer-review

50 Citations (Scopus)

440 Downloads (Pure)

ENCORE: Software for Quantitative Ensemble Comparison

Tiberti, M., Papaleo, E., Bengtsen, T., Boomsma, W. K. & Lindorff-Larsen, K., 2015, In: PLoS Computational Biology. 11, 10, 16 p., e1004415.

Research output: Contribution to journal › Journal article › Research › peer-review

34 Citations (Scopus)

76 Downloads (Pure)

Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

Bugge, K. Ø., Steinocher, H., Brooks, A. J., Lindorff-Larsen, K. & Kragelund, B. B., 15 Sept 2015, In: Analytical Chemistry. 87, 18, p. 9126–9131 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

6 Citations (Scopus)

Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

Sborgi, L., Verma, A., Piana, S., Lindorff-Larsen, K., Cerminara, M., Santiveri, C. M., Shaw, D. E., De Alba, E. & Muñoz, V., 2015, In: Journal of the American Chemical Society. 137, 20, p. 6506-6516 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

58 Citations (Scopus)

37 Downloads (Pure)

Structure of a functional amyloid protein subunit computed using sequence variation

Tian, P., Boomsma, W. K., Wang, Y., Otzen, D., Jensen, M. H. & Lindorff-Larsen, K., 14 Jan 2015, In: Journal of the American Chemical Society. 137, 1, p. 22–25 4 p.

Research output: Contribution to journal › Journal article › Research › peer-review

66 Citations (Scopus)

What does evolution tell us about the structure of a functional amyloid protein?

Tian, P., Boomsma, W. K., Wang, Y., Otzen, D. E., Jensen, M. H. & Lindorff-Larsen, K., 2015, In: Biophysical Journal. 108, 2, Supplement 1, p. 227a 1 p.

Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

2014

CECAM workshop on intrinsically disordered proteins

Rösner, H. I., Papaleo, E., Haxholm, G. W., Best, R. B., Kragelund, B. B. & Lindorff-Larsen, K., 2014, In: Intrinsically Disordered Proteins. 2, 1, p. 1-5 5 p.

Research output: Contribution to journal › Conference abstract in journal › Research

466 Downloads (Pure)

Combining experiments and simulations using the maximum entropy principle

Boomsma, W. K., Ferkinghoff-Borg, J. & Lindorff-Larsen, K., Feb 2014, In: PLoS Computational Biology. 10, 2, 9 p., e1003406.

Research output: Contribution to journal › Journal article › Research › peer-review

110 Citations (Scopus)

553 Downloads (Pure)

Communication routes in ARID domains between distal residues in Helix 5 and the DNA-binding loops

Invernizzi, G., Tiberti, M., Lambrughi, M., Lindorff-Larsen, K. & Papaleo, E., 1 Sept 2014, In: P L o S Computational Biology (Online). 10, 9, 13 p., e1003744.

Research output: Contribution to journal › Journal article › Research › peer-review

23 Citations (Scopus)

370 Downloads (Pure)

Conformational changes and free energies in a Proline isomerase

Papaleo, E., Sutto, L., Gervasio, F. L. & Lindorff-Larsen, K., 9 Sept 2014, In: Journal of Chemical Theory and Computation. 10, 9, p. 4169-4174 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

29 Citations (Scopus)

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

Boomsma, W. K., Tian, P., Frellsen, J., Ferkinghoff-Borg, J., Hamelryck, T. W., Lindorff-Larsen, K. & Vendruscolo, M., 23 Sept 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 38, p. 13852-13857 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

23 Citations (Scopus)

Probabilistic determination of native state ensembles of proteins

Olsson, S., Vögeli, B. R., Cavalli, A., Boomsma, W. K., Ferkinghoff-Borg, J., Lindorff-Larsen, K. & Hamelryck, T. W., 12 Aug 2014, In: Journal of Chemical Theory and Computation. 10, 8, p. 3484-3491 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

33 Citations (Scopus)

Robust estimation of diffusion-optimized ensembles for enhanced sampling

Tian, P., Jónsson, S. Æ., Ferkinghoff-Borg, J., Krivov, S. V. ., Lindorff-Larsen, K., Irbäck, A. & Boomsma, W. K., 11 Feb 2014, In: Journal of Chemical Theory and Computation. 10, 2, p. 543–553 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

10 Citations (Scopus)

2013

A sticky cage can slow down folding

Boomsma, W. & Lindorff-Larsen, K., 5 Mar 2013, In: Biophysical Journal. 104, 5, p. 964-965 2 p.

Research output: Contribution to journal › Comment/debate › Research

1 Citation (Scopus)

Atomic-level description of ubiquitin folding

Piana, S., Lindorff-Larsen, K. & Shaw, D. E., 9 Apr 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 15, p. 5915-5920 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

218 Citations (Scopus)

Atomistic description of the folding of a dimeric protein

Piana, S., Lindorff-Larsen, K. & Shaw, D. E., 24 Oct 2013, In: Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical. 117, 42, p. 12935-12942 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

31 Citations (Scopus)

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

Boomsma, W. K., Frellsen, J., Harder, T. P., Bottaro, S., Johansson, K. E., Tian, P., Stovgaard, K., Andreetta, C., Olsson, S., Valentin, J., Antonov, L. D., Christensen, A. S., Borg, M., Jensen, J. H., Lindorff-Larsen, K., Ferkinghoff-Borg, J. & Hamelryck, T. W., 15 Jul 2013, In: Journal of Computational Chemistry. 34, 19, p. 1697-1705 9 p.

Research output: Contribution to journal › Journal article › Research › peer-review

31 Citations (Scopus)

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

Christensen, A. S., Linnet, T. E., Borg, M., Boomsma, W. K., Lindorff-Larsen, K., Hamelryck, T. W. & Jensen, J. H., 31 Dec 2013, In: PLoS ONE. 8, 12, 10 p., e84123.

Research output: Contribution to journal › Journal article › Research › peer-review

17 Citations (Scopus)

2027 Downloads (Pure)

The Structure of the Central Side Chain is Crucial for Anoplin Hemolytic Activity

Munk, J., Thøgersen, L., Uggerhøj, L. E., Wimmer, R., Frimodt-Møller, N., Lindorff-Larsen, K. & Hansen, P. R., 2013, Proceedings of the 23rd American Peptide Symposium. Lebl, M. (ed.). American Peptide Society

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data

Bottaro, S., Lindorff-Larsen, K. & Best, R. B., 10 Dec 2013, In: Journal of Chemical Theory and Computation. 9, 12, p. 5641-5652 12 p.

Research output: Contribution to journal › Journal article › Research › peer-review

29 Citations (Scopus)

2012

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations

Piana, S., Lindorff-Larsen, K., Dirks, R. M., Salmon, J. K., Dror, R. O. & Shaw, D. E., 29 Jun 2012, In: P L o S One. 7, 6, 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

67 Citations (Scopus)

759 Downloads (Pure)

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

Papaleo, E., Lindorff-Larsen, K. & Gioia, L. D., 28 Sept 2012, In: Physical Chemistry Chemical Physics. 14, p. 12515-12525 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

24 Citations (Scopus)

Protein folding kinetics and thermodynamics from atomistic simulation

Piana, S., Lindorff-Larsen, K. & Shaw, D. E., 30 Oct 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 44, p. 17845-17850 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

189 Citations (Scopus)

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

Lindorff-Larsen, K., Trbovic, N., Maragakis, P., Piana, S. & Shaw, D. E., 29 Feb 2012, In: Journal of the American Chemical Society. 134, 8, p. 3787-3791 5 p.

Research output: Contribution to journal › Journal article › Research › peer-review

182 Citations (Scopus)

Systematic validation of protein force fields against experimental data

Lindorff-Larsen, K., Maragakis, P., Piana, S., Eastwood, M. P., Dror, R. O. & Shaw, D. E., 22 Feb 2012, In: P L o S One. 7, 2, 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

461 Citations (Scopus)

383 Downloads (Pure)

2011

Computational design and experimental testing of the fastest-folding ß-sheet protein

Piana, S., Sarkar, K., Lindorff-Larsen, K., Guo, M., Gruebele, M. & Shaw, D. E., 7 Jan 2011, In: Journal of Molecular Biology. 405, 1, p. 43-48 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

90 Citations (Scopus)

How fast-folding proteins fold

Lindorff-Larsen, K., Piana, S., Dror, R. O. & Shaw, D. E., 28 Oct 2011, In: Science (New York, N.Y.). 334, 6055, p. 517-20 4 p.

Research output: Contribution to journal › Journal article › Research › peer-review

1155 Citations (Scopus)

How robust are protein folding simulations with respect to force field parameterization?

Piana, S., Lindorff-Larsen, K. & Shaw, D. E., 4 May 2011, In: Biophysical Journal (2011). 100, 9, p. L47-L49

Research output: Contribution to journal › Journal article › Research › peer-review

551 Citations (Scopus)

2010

Atomic-level characterization of the structural dynamics of proteins

Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y. & Wriggers, W., 15 Oct 2010, In: Science (New York, N.Y.). 330, 6002, p. 341-6 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

1209 Citations (Scopus)

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O. & Shaw, D. E., Jun 2010, In: Proteins: Structure, Function, and Bioinformatics. 78, 8, p. 1950-8 9 p.

Research output: Contribution to journal › Journal article › Research › peer-review

2849 Citations (Scopus)

Principles of conduction and hydrophobic gating in K+ channels

Jensen, M. Ø., Borhani, D. W., Lindorff-Larsen, K., Maragakis, P., Jogini, V., Eastwood, M. P., Dror, R. O. & Shaw, D. E., 30 Mar 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 13, p. 5833-8 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

225 Citations (Scopus)

2009

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations

Wriggers, W., Stafford, K. A., Shan, Y., Piana, S., Maragakis, P., Lindorff-Larsen, K., Miller, P. J., Gullingsrud, J., Rendleman, C. A., Eastwood, M. P., Dror, R. O. & Shaw, D. E., 1 Oct 2009, In: Journal of Chemical Theory and Computation. 5, 10, p. 2595-2605 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

43 Citations (Scopus)

Long-timescale molecular dynamics simulations of protein structure and function

Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O. & Shaw, D. E., 2009, In: Current Opinion in Structural Biology. 19, 2, p. 120-7 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

519 Citations (Scopus)

Millisecond-scale molecular dynamics simulations on Anton

Shaw, D. E., Dror, R. O., Salmon, J. K., Grossman, J. P., Mackenzie, K. M., Bank, J. A., Young, C., Deneroff, M. M., Batson, B., Bowers, K. J., Chow, E., Eastwood, M. P., Ierardi, D., Klepeis, J. L., Kuskin, J., Larson, R. H., Lindorff-Larsen, K., Maragakis, P., Moraes, M. A., Piana, S., & 2 othersShan, Y. & Towles, B., 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis. Association for Computing Machinery, 11 p.

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

283 Citations (Scopus)

Similarity measures for protein ensembles

Lindorff-Larsen, K. & Ferkinghoff-Borg, J., 2009, In: PLoS ONE. 4, 1, 13 p., e4203.

Research output: Contribution to journal › Journal article › Research › peer-review

43 Citations (Scopus)

794 Downloads (Pure)

2008

Experimental parameterization of an energy function for the simulation of unfolded proteins

Nørgaard, A. B., Ferkinghoff-Borg, J. & Lindorff-Larsen, K., 2008, In: Biophysical Journal. 94, 1, p. 182-192

Research output: Contribution to journal › Journal article › Research › peer-review

35 Citations (Scopus)

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

Maragakis, P., Lindorff-Larsen, K., Eastwood, M. P., Dror, R. O., Klepeis, J. L., Arkin, I. T., Jensen, M. Ø., Xu, H., Trbovic, N., Friesner, R. A., Iii, A. G. P. & Shaw, D. E., 2008, In: Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical. 112, 19, p. 6155-6158 4 p.

Research output: Contribution to journal › Journal article › Research › peer-review

166 Citations (Scopus)

2007

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins

Geierhaas, C. D., Nickson, A. A., Lindorff-Larsen, K., Clarke, J. & Vendruscolo, M., 2007, In: Protein Science. 16, 1, p. 125-34 10 p.

Research output: Contribution to journal › Journal article › Research › peer-review

40 Citations (Scopus)

Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis.

Modig, K., Jürgensen, V. W., Lindorff-Larsen, K., Fieber, W., Bohr, H. G. & Poulsen, F. M., 2007, In: FEBS Letters. 581, 25, p. 4965-4971 7 p.

Research output: Contribution to journal › Journal article › Research › peer-review

42 Citations (Scopus)

2006

Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

Francis, C. J., Lindorff-Larsen, K., Best, R. B. & Bendruscolo, M., 2006, In: Proteins - Structure Function and Bioinformatics. 65, 1, p. 145-52

Research output: Contribution to journal › Journal article › Research › peer-review

38 Citations (Scopus)

Conformational fluctuations affect protein alignment in dilute liquid crystal media.

Louhivuori, M., Otten, R., Lindorff-Larsen, K. & Annila, A., 2006, In: Journal of the American Chemical Society. 128, 13, p. 4371-4376 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

22 Citations (Scopus)

Relation between native ensembles and experimental structures of proteins.

Best, R. B., Lindorff-Larsen, K., DePristo, M. A. & VEndruscolo, M., 2006, In: Proceedings of the National Academy of Science of the United States of America. 103, 29, p. 10901-6

Research output: Contribution to journal › Journal article › Research › peer-review

110 Citations (Scopus)

Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition

Chandran, V., Stollar, E. J., Lindorff-Larsen, K., Harper, J. F., Chazin, W. J., Dobson, C. M., Luisi, B. F. & Christodoulou, J., 2006, In: Journal of Molecular Biology. 357, 2, p. 400-10 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

49 Citations (Scopus)

2005

Formation of Native and Non-native Interactions in Ensembles of Denatured ACBP Molecules from Paramagnetic Relaxation Enhancement Studies

Kristjansdottir, S., Lindorff-Larsen, K., Fieber, W., Dobson, C. M., Vendruscolo, M. & Poulsen, F. M., 2005, In: Journal of Molecular Biology. 347, 5, p. 1053-1062

Research output: Contribution to journal › Journal article › Research › peer-review

86 Citations (Scopus)

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

Lindorff-Larsen, K., Best, R. B. & Vendruscolo, M., 2005, In: Journal of Biomolecular NMR. 32, 4, p. 273-280

Research output: Contribution to journal › Journal article › Research › peer-review

34 Citations (Scopus)

Kresten Lindorff-Larsen

Research output

Search results