Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 129

1.

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome.

Abildgaard AB, Stein A, Nielsen SV, Schultz-Knudsen K, Papaleo E, Shrikhande A, Hoffmann ER, Bernstein I, Gerdes AM, Takahashi M, Ishioka C, Lindorff-Larsen K, Hartmann-Petersen R.

Elife. 2019 Nov 7;8. pii: e49138. doi: 10.7554/eLife.49138.

2.

Allosteric modulation of the sarcoplasmic reticulum Ca2+ ATPase by thapsigargin via decoupling of functional motions.

Saleh N, Wang Y, Nissen P, Lindorff-Larsen K.

Phys Chem Chem Phys. 2019 Oct 9;21(39):21991-21995. doi: 10.1039/c9cp04736k.

PMID:
31552962
3.

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.

Pedersen DV, Gadeberg TAF, Thomas C, Wang Y, Joram N, Jensen RK, Mazarakis SMM, Revel M, El Sissy C, Petersen SV, Lindorff-Larsen K, Thiel S, Laursen NS, Fremeaux-Bacchi V, Andersen GR.

Front Immunol. 2019 Aug 22;10:2007. doi: 10.3389/fimmu.2019.02007. eCollection 2019.

4.

Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome.

Karstensen HG, Rendtorff ND, Hindbæk LS, Colombo R, Stein A, Birkebæk NH, Hartmann-Petersen R, Lindorff-Larsen K, Højland AT, Petersen MB, Tranebjærg L.

Eur J Med Genet. 2019 Aug 23:103733. doi: 10.1016/j.ejmg.2019.103733. [Epub ahead of print]

PMID:
31449985
5.

Substrate-induced conformational dynamics of the dopamine transporter.

Nielsen AK, Möller IR, Wang Y, Rasmussen SGF, Lindorff-Larsen K, Rand KD, Loland CJ.

Nat Commun. 2019 Jun 20;10(1):2714. doi: 10.1038/s41467-019-10449-w.

6.

Risk of post-colonoscopy colorectal cancer in Denmark: time trends and comparison with Sweden and the English National Health Service.

Pedersen L, Valori R, Bernstein I, Lindorff-Larsen K, Green C, Torp-Pedersen C.

Endoscopy. 2019 Aug;51(8):733-741. doi: 10.1055/a-0919-4803. Epub 2019 Jun 7.

PMID:
31174223
7.

Fitting Corrections to an RNA Force Field Using Experimental Data.

Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Šponer J, Bussi G.

J Chem Theory Comput. 2019 Jun 11;15(6):3425-3431. doi: 10.1021/acs.jctc.9b00206. Epub 2019 May 23.

PMID:
31050905
8.

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor.

Escobedo A, Topal B, Kunze MBA, Aranda J, Chiesa G, Mungianu D, Bernardo-Seisdedos G, Eftekharzadeh B, Gairí M, Pierattelli R, Felli IC, Diercks T, Millet O, García J, Orozco M, Crehuet R, Lindorff-Larsen K, Salvatella X.

Nat Commun. 2019 May 2;10(1):2034. doi: 10.1038/s41467-019-09923-2.

9.

Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1.

Lückmann M, Trauelsen M, Bentsen MA, Nissen TAD, Martins J, Fallah Z, Nygaard MM, Papaleo E, Lindorff-Larsen K, Schwartz TW, Frimurer TM.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):7123-7128. doi: 10.1073/pnas.1811066116. Epub 2019 Mar 14.

10.

Biophysical and Mechanistic Models for Disease-Causing Protein Variants.

Stein A, Fowler DM, Hartmann-Petersen R, Lindorff-Larsen K.

Trends Biochem Sci. 2019 Jul;44(7):575-588. doi: 10.1016/j.tibs.2019.01.003. Epub 2019 Jan 31. Review.

PMID:
30712981
11.

Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations.

Scheller R, Stein A, Nielsen SV, Marin FI, Gerdes AM, Di Marco M, Papaleo E, Lindorff-Larsen K, Hartmann-Petersen R.

Hum Mutat. 2019 Apr;40(4):444-457. doi: 10.1002/humu.23707. Epub 2019 Jan 25.

PMID:
30648773
12.

Protein stability and degradation in health and disease.

Clausen L, Abildgaard AB, Gersing SK, Stein A, Lindorff-Larsen K, Hartmann-Petersen R.

Adv Protein Chem Struct Biol. 2019;114:61-83. doi: 10.1016/bs.apcsb.2018.09.002. Epub 2018 Nov 28. Review.

PMID:
30635086
13.

Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.

Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P.

Cell. 2018 Nov 15;175(5):1365-1379.e25. doi: 10.1016/j.cell.2018.10.039.

14.

Barnaba: software for analysis of nucleic acid structures and trajectories.

Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K.

RNA. 2019 Feb;25(2):219-231. doi: 10.1261/rna.067678.118. Epub 2018 Nov 12.

PMID:
30420522
15.

Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments.

Bouchard JJ, Otero JH, Scott DC, Szulc E, Martin EW, Sabri N, Granata D, Marzahn MR, Lindorff-Larsen K, Salvatella X, Schulman BA, Mittag T.

Mol Cell. 2018 Oct 4;72(1):19-36.e8. doi: 10.1016/j.molcel.2018.08.027. Epub 2018 Sep 20.

16.

A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel.

Santner P, Martins JMDS, Laursen JS, Behrendt L, Riber L, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K.

Biochemistry. 2018 Oct 16;57(41):5949-5956. doi: 10.1021/acs.biochem.8b00721. Epub 2018 Oct 3.

PMID:
30230312
17.

Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants.

Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K.

Biochemistry. 2018 Oct 16;57(41):5957-5968. doi: 10.1021/acs.biochem.8b00722. Epub 2018 Oct 3.

PMID:
30230310
18.

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias.

Wang Y, Tian P, Boomsma W, Lindorff-Larsen K.

J Phys Chem B. 2018 Dec 13;122(49):11174-11185. doi: 10.1021/acs.jpcb.8b06335. Epub 2018 Sep 6.

PMID:
30141937
19.

Frequency adaptive metadynamics for the calculation of rare-event kinetics.

Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K.

J Chem Phys. 2018 Aug 21;149(7):072309. doi: 10.1063/1.5024679.

PMID:
30134721
20.

Biophysical experiments and biomolecular simulations: A perfect match?

Bottaro S, Lindorff-Larsen K.

Science. 2018 Jul 27;361(6400):355-360. doi: 10.1126/science.aat4010. Review.

PMID:
30049874
21.

Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts.

Kassem MM, Christoffersen LB, Cavalli A, Lindorff-Larsen K.

Sci Rep. 2018 Jul 24;8(1):11112. doi: 10.1038/s41598-018-29357-y.

22.

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs.

Papaleo E, Camilloni C, Teilum K, Vendruscolo M, Lindorff-Larsen K.

PeerJ. 2018 Jul 4;6:e5125. doi: 10.7717/peerj.5125. eCollection 2018.

23.

How well do force fields capture the strength of salt bridges in proteins?

Ahmed MC, Papaleo E, Lindorff-Larsen K.

PeerJ. 2018 Jun 11;6:e4967. doi: 10.7717/peerj.4967. eCollection 2018.

24.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K.

Sci Adv. 2018 May 18;4(5):eaar8521. doi: 10.1126/sciadv.aar8521. eCollection 2018 May.

25.

Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level.

Best RB, Lindorff-Larsen K.

Curr Opin Struct Biol. 2018 Apr;49:iv-v. doi: 10.1016/j.sbi.2018.04.002. No abstract available.

26.

Dynamic activation and regulation of the mitogen-activated protein kinase p38.

Kumar GS, Clarkson MW, Kunze MBA, Granata D, Wand AJ, Lindorff-Larsen K, Page R, Peti W.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):4655-4660. doi: 10.1073/pnas.1721441115. Epub 2018 Apr 16.

27.

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics.

Wang Y, Martins JM, Lindorff-Larsen K.

Chem Sci. 2017 Sep 1;8(9):6466-6473. doi: 10.1039/c7sc01627a. Epub 2017 Jul 12.

28.

Consensus on procedures to include in a simulation-based curriculum in ophthalmology: a national Delphi study.

Thomsen ASS, la Cour M, Paltved C, Lindorff-Larsen KG, Nielsen BU, Konge L, Nayahangan LJ.

Acta Ophthalmol. 2018 Aug;96(5):519-527. doi: 10.1111/aos.13700. Epub 2018 Mar 25.

29.

On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations.

Henriques J, Arleth L, Lindorff-Larsen K, Skepö M.

J Mol Biol. 2018 Aug 3;430(16):2521-2539. doi: 10.1016/j.jmb.2018.03.002. Epub 2018 Mar 14.

PMID:
29548755
30.

Structural heterogeneity and dynamics in protein evolution and design.

Johansson KE, Lindorff-Larsen K.

Curr Opin Struct Biol. 2018 Feb;48:157-163. doi: 10.1016/j.sbi.2018.01.010. Epub 2018 Feb 3. Review.

PMID:
29413956
31.

Determining procedures for simulation-based training in radiology: a nationwide needs assessment.

Nayahangan LJ, Nielsen KR, Albrecht-Beste E, Bachmann Nielsen M, Paltved C, Lindorff-Larsen KG, Nielsen BU, Konge L.

Eur Radiol. 2018 Jun;28(6):2319-2327. doi: 10.1007/s00330-017-5244-7. Epub 2018 Jan 9.

PMID:
29318426
32.

Role of protein dynamics in transmembrane receptor signalling.

Wang Y, Bugge K, Kragelund BB, Lindorff-Larsen K.

Curr Opin Struct Biol. 2018 Feb;48:74-82. doi: 10.1016/j.sbi.2017.10.017. Epub 2017 Nov 11. Review.

PMID:
29136528
33.

An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations.

Nygaard M, Kragelund BB, Papaleo E, Lindorff-Larsen K.

Biophys J. 2017 Aug 8;113(3):550-557. doi: 10.1016/j.bpj.2017.06.042.

34.

Blocking protein quality control to counter hereditary cancers.

Kampmeyer C, Nielsen SV, Clausen L, Stein A, Gerdes AM, Lindorff-Larsen K, Hartmann-Petersen R.

Genes Chromosomes Cancer. 2017 Dec;56(12):823-831. doi: 10.1002/gcc.22487. Epub 2017 Sep 6. Review.

PMID:
28779490
35.

Mapping the Universe of RNA Tetraloop Folds.

Bottaro S, Lindorff-Larsen K.

Biophys J. 2017 Jul 25;113(2):257-267. doi: 10.1016/j.bpj.2017.06.011. Epub 2017 Jun 30.

36.

A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1).

Hendus-Altenburger R, Lambrughi M, Terkelsen T, Pedersen SF, Papaleo E, Lindorff-Larsen K, Kragelund BB.

Cell Signal. 2017 Sep;37:40-51. doi: 10.1016/j.cellsig.2017.05.015. Epub 2017 May 26.

37.

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations.

Nielsen SV, Stein A, Dinitzen AB, Papaleo E, Tatham MH, Poulsen EG, Kassem MM, Rasmussen LJ, Lindorff-Larsen K, Hartmann-Petersen R.

PLoS Genet. 2017 Apr 19;13(4):e1006739. doi: 10.1371/journal.pgen.1006739. eCollection 2017 Apr.

38.

A National Needs Assessment to Identify Technical Procedures in Vascular Surgery for Simulation Based Training.

Nayahangan LJ, Konge L, Schroeder TV, Paltved C, Lindorff-Larsen KG, Nielsen BU, Eiberg JP.

Eur J Vasc Endovasc Surg. 2017 Apr;53(4):591-599. doi: 10.1016/j.ejvs.2017.01.011. Epub 2017 Mar 1.

39.

Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.

Choy MS, Li Y, Machado LESF, Kunze MBA, Connors CR, Wei X, Lindorff-Larsen K, Page R, Peti W.

Mol Cell. 2017 Feb 16;65(4):644-658.e5. doi: 10.1016/j.molcel.2017.01.014.

40.

Diversity-Oriented Peptide Stapling: A Third Generation Copper-Catalysed Azide-Alkyne Cycloaddition Stapling and Functionalisation Strategy.

Tran PT, Larsen CØ, Røndbjerg T, De Foresta M, Kunze MB, Marek A, Løper JH, Boyhus LE, Knuhtsen A, Lindorff-Larsen K, Pedersen DS.

Chemistry. 2017 Mar 8;23(14):3490-3495. doi: 10.1002/chem.201700128. Epub 2017 Feb 16.

PMID:
28106305
41.

Optimizing protein and energy intake in hospitals by improving individualized meal serving, hosting and the eating environment.

Holst M, Beermann T, Mortensen MN, Skadhauge LB, Køhler M, Lindorff-Larsen K, Rasmussen HH.

Nutrition. 2017 Feb;34:14-20. doi: 10.1016/j.nut.2016.05.011. Epub 2016 Jun 8.

PMID:
28063508
42.

Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data.

Bottaro S, Lindorff-Larsen K, Best RB.

J Chem Theory Comput. 2017 Jan 10;13(1):392. doi: 10.1021/acs.jctc.6b01188. Epub 2016 Dec 19. No abstract available.

43.

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.

Lambrughi M, De Gioia L, Gervasio FL, Lindorff-Larsen K, Nussinov R, Urani C, Bruschi M, Papaleo E.

Nucleic Acids Res. 2016 Nov 2;44(19):9096-9109. Epub 2016 Sep 6.

44.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

Johansson KE, Tidemand Johansen N, Christensen S, Horowitz S, Bardwell JCA, Olsen JG, Willemoës M, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T, Winther JR.

J Mol Biol. 2016 Oct 23;428(21):4361-4377. doi: 10.1016/j.jmb.2016.09.013. Epub 2016 Sep 20.

45.

Mapping transiently formed and sparsely populated conformations on a complex energy landscape.

Wang Y, Papaleo E, Lindorff-Larsen K.

Elife. 2016 Aug 23;5. pii: e17505. doi: 10.7554/eLife.17505.

46.

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

Bugge K, Lindorff-Larsen K, Kragelund BB.

FEBS J. 2016 Dec;283(24):4424-4451. doi: 10.1111/febs.13793. Epub 2016 Jul 18. Review.

47.

A Soluble, Folded Protein without Charged Amino Acid Residues.

Højgaard C, Kofoed C, Espersen R, Johansson KE, Villa M, Willemoës M, Lindorff-Larsen K, Teilum K, Winther JR.

Biochemistry. 2016 Jul 19;55(28):3949-56. doi: 10.1021/acs.biochem.6b00269. Epub 2016 Jul 6.

PMID:
27307139
48.

Identifying Technical Procedures in Pulmonary Medicine That Should Be Integrated in a Simulation-Based Curriculum: A National General Needs Assessment.

Nayahangan LJ, Clementsen PF, Paltved C, Lindorff-Larsen KG, Nielsen BU, Konge L.

Respiration. 2016;91(6):517-22. doi: 10.1159/000446926. Epub 2016 Jun 9.

49.

Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.

Kassem MM, Wang Y, Boomsma W, Lindorff-Larsen K.

Biophys J. 2016 Jun 7;110(11):2342-2348. doi: 10.1016/j.bpj.2016.04.039.

50.

A combined computational and structural model of the full-length human prolactin receptor.

Bugge K, Papaleo E, Haxholm GW, Hopper JT, Robinson CV, Olsen JG, Lindorff-Larsen K, Kragelund BB.

Nat Commun. 2016 May 13;7:11578. doi: 10.1038/ncomms11578.

Supplemental Content

Loading ...
Support Center