Kresten Lindorff-Larsen - Publications

Affiliations: 
Biology University of Copenhagen, København, Denmark 

193 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
2022 Orioli S, Henning Hansen CG, Lindorff-Larsen K. Transient exposure of a buried phosphorylation site in an autoinhibited protein. Biophysical Journal. 121: 91-101. PMID 34864046 DOI: 10.1016/j.bpj.2021.11.2890  1
2021 Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Lindorff-Larsen K, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7  1
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  1
2021 Zutz A, Hamborg L, Pedersen LE, Kassem MM, Papaleo E, Koza A, Herrgård MJ, Jensen SI, Teilum K, Lindorff-Larsen K, Nielsen AT. A dual-reporter system for investigating and optimizing protein translation and folding in E. coli. Nature Communications. 12: 6093. PMID 34667164 DOI: 10.1038/s41467-021-26337-1  1
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  1
2021 Marin FI, Johansson KE, O'Shea C, Lindorff-Larsen K, Winther JR. Computational and Experimental Assessment of Backbone Templates for Computational Redesign of the Thioredoxin Fold. The Journal of Physical Chemistry. B. 125: 11141-11149. PMID 34592819 DOI: 10.1021/acs.jpcb.1c05528  1
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  1
2021 Newcombe EA, Fernandes CB, Lundsgaard JE, Brakti I, Lindorff-Larsen K, Langkilde AE, Skriver K, Kragelund BB. Insight into Calcium-Binding Motifs of Intrinsically Disordered Proteins. Biomolecules. 11. PMID 34439840 DOI: 10.3390/biom11081173  1
2021 Madland E, Forsberg Z, Wang Y, Lindorff-Larsen K, Niebisch A, Modregger J, Eijsink VGH, Aachmann FL, Courtade G. Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus. The Journal of Biological Chemistry. 101084. PMID 34411561 DOI: 10.1016/j.jbc.2021.101084  1
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  1
2021 Lambrughi M, Maiani E, Aykac Fas B, Shaw GS, Kragelund BB, Lindorff-Larsen K, Teilum K, Invernizzi G, Papaleo E. Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs. Frontiers in Molecular Biosciences. 8: 676235. PMID 34262938 DOI: 10.3389/fmolb.2021.676235  1
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  1
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  1
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  1
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  1
2021 Wang K, Dagil R, Lavstsen T, Misra SK, Spliid CB, Wang Y, Gustavsson T, Sandoval DR, Vidal-Calvo EE, Choudhary S, Agerbaek MØ, Lindorff-Larsen K, Nielsen MA, Theander TG, Sharp JS, et al. Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding. Nature Communications. 12: 2956. PMID 34011972 DOI: 10.1038/s41467-021-23254-1  1
2021 Wang K, Dagil R, Lavstsen T, Misra SK, Spliid CB, Wang Y, Gustavsson T, Sandoval DR, Vidal-Calvo EE, Choudhary S, Agerbaek MØ, Lindorff-Larsen K, Nielsen MA, Theander TG, Sharp JS, et al. Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding. Nature Communications. 12: 2956. PMID 34011972 DOI: 10.1038/s41467-021-23254-1  1
2021 Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and assembly dynamics of the essential mitochondrial chaperone complex TIM9·10·12. Structure (London, England : 1993). PMID 33974880 DOI: 10.1016/j.str.2021.04.009  1
2021 Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and assembly dynamics of the essential mitochondrial chaperone complex TIM9·10·12. Structure (London, England : 1993). PMID 33974880 DOI: 10.1016/j.str.2021.04.009  1
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  1
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  1
2021 Gersing SK, Wang Y, Grønbæk-Thygesen M, Kampmeyer C, Clausen L, Willemoës M, Andréasson C, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Mapping the degradation pathway of a disease-linked aspartoacylase variant. Plos Genetics. 17: e1009539. PMID 33914734 DOI: 10.1371/journal.pgen.1009539  1
2021 Gersing SK, Wang Y, Grønbæk-Thygesen M, Kampmeyer C, Clausen L, Willemoës M, Andréasson C, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Mapping the degradation pathway of a disease-linked aspartoacylase variant. Plos Genetics. 17: e1009539. PMID 33914734 DOI: 10.1371/journal.pgen.1009539  1
2021 Nielsen SV, Hartmann-Petersen R, Stein A, Lindorff-Larsen K. Multiplexed assays reveal effects of missense variants in MSH2 and cancer predisposition. Plos Genetics. 17: e1009496. PMID 33886538 DOI: 10.1371/journal.pgen.1009496  1
2021 Cagiada M, Johansson KE, Valanciute A, Nielsen SV, Hartmann-Petersen R, Yang JJ, Fowler DM, Stein A, Lindorff-Larsen K. Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance. Molecular Biology and Evolution. PMID 33779753 DOI: 10.1093/molbev/msab095  1
2021 Lindorff-Larsen K, Teilum K. Linking thermodynamics and measurements of protein stability. Protein Engineering, Design & Selection : Peds. 34. PMID 33724431 DOI: 10.1093/protein/gzab002  1
2021 Martin EW, Thomasen FE, Milkovic NM, Cuneo MJ, Grace CR, Nourse A, Lindorff-Larsen K, Mittag T. Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation. Nucleic Acids Research. PMID 33577679 DOI: 10.1093/nar/gkab063  1
2021 Hervø-Hansen S, Højgaard C, Johansson KE, Wang Y, Wahni K, Young D, Messens J, Teilum K, Lindorff-Larsen K, Winther JR. Charge Interactions in a Highly Charge-Depleted Protein. Journal of the American Chemical Society. PMID 33529004 DOI: 10.1021/jacs.0c10789  1
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  1
2021 Pedersen DV, Pedersen MN, Mazarakis SM, Wang Y, Lindorff-Larsen K, Arleth L, Andersen GR. Properdin oligomers adopt rigid extended conformations supporting function. Elife. 10. PMID 33480354 DOI: 10.7554/eLife.63356  1
2020 Sučec I, Wang Y, Dakhlaoui O, Weinhäupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B, Schanda P. Structural basis of client specificity in mitochondrial membrane-protein chaperones. Science Advances. 6. PMID 33355130 DOI: 10.1126/sciadv.abd0263  1
2020 Henriques J, Lindorff-Larsen K. Protein Dynamics Enables Phosphorylation of Buried Residues in Cdk2/Cyclin-A-Bound p27. Biophysical Journal. 119: 2010-2018. PMID 33147476 DOI: 10.1016/j.bpj.2020.06.040  1
2020 Clausen L, Stein A, Grønbæk-Thygesen M, Nygaard L, Søltoft CL, Nielsen SV, Lisby M, Ravid T, Lindorff-Larsen K, Hartmann-Petersen R. Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation. Plos Genetics. 16: e1009187. PMID 33137092 DOI: 10.1371/journal.pgen.1009187  1
2020 Abildgaard AB, Gersing SK, Larsen-Ledet S, Nielsen SV, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome. Biomolecules. 10. PMID 32759676 DOI: 10.3390/biom10081141  1
2020 Hamborg L, Horsted EW, Johansson KE, Willemoës M, Lindorff-Larsen K, Teilum K. Global analysis of protein stability by temperature and chemical denaturation. Analytical Biochemistry. 113863. PMID 32738214 DOI: 10.1016/J.Ab.2020.113863  1
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  1
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  1
2020 Ahmed MC, Crehuet R, Lindorff-Larsen K. Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins. Methods in Molecular Biology (Clifton, N.J.). 2141: 429-445. PMID 32696370 DOI: 10.1007/978-1-0716-0524-0_21  1
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  1
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  1
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  1
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  1
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  1
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  1
2020 Fraser JS, Lindorff-Larsen K, Bonomi M. What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? Journal of Chemical Information and Modeling. PMID 32090567 DOI: 10.1021/Acs.Jcim.0C00123  0.01
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  1
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  1
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  1
2019 Lindorff-Larsen K. Dissecting the statistical properties of the linear extrapolation method of determining protein stability. Protein Engineering, Design & Selection : Peds. 32: 471-479. PMID 32399570 DOI: 10.1093/protein/gzaa010  0.01
2019 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. Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome. Elife. 8. PMID 31697235 DOI: 10.7554/eLife.49138  1
2019 Saleh N, Wang Y, Nissen P, Lindorff-Larsen K. Allosteric modulation of the sarcoplasmic reticulum Ca ATPase by thapsigargin via decoupling of functional motions. Physical Chemistry Chemical Physics : Pccp. PMID 31552962 DOI: 10.1039/c9cp04736k  1
2019 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. Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Frontiers in Immunology. 10: 2007. PMID 31507604 DOI: 10.3389/fimmu.2019.02007  1
2019 Karstensen HG, Rendtorff ND, Hindbæk LS, Colombo R, Stein A, Birkebæk NH, Hartmann-Petersen R, Lindorff-Larsen K, Højland AT, Petersen MB, Tranebjærg L. Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome. European Journal of Medical Genetics. 103733. PMID 31449985 DOI: 10.1016/j.ejmg.2019.103733  1
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  1
2019 Nielsen AK, Möller IR, Wang Y, Rasmussen SGF, Lindorff-Larsen K, Rand KD, Loland CJ. Substrate-induced conformational dynamics of the dopamine transporter. Nature Communications. 10: 2714. PMID 31221956 DOI: 10.1038/s41467-019-10449-w  1
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  1
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  1
2019 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, ... ... Lindorff-Larsen K, et al. Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor. Nature Communications. 10: 2034. PMID 31048691 DOI: 10.1038/S41467-019-09923-2  1
2019 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, ... ... Lindorff-Larsen K, et al. Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor. Nature Communications. 10: 2034. PMID 31048691 DOI: 10.1038/S41467-019-09923-2  1
2019 Lückmann M, Trauelsen M, Bentsen MA, Nissen TAD, Martins J, Fallah Z, Nygaard MM, Papaleo E, Lindorff-Larsen K, Schwartz TW, Frimurer TM. 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. PMID 30872479 DOI: 10.1073/pnas.1811066116  1
2019 Lückmann M, Trauelsen M, Bentsen MA, Nissen TAD, Martins J, Fallah Z, Nygaard MM, Papaleo E, Lindorff-Larsen K, Schwartz TW, Frimurer TM. 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. PMID 30872479 DOI: 10.1073/pnas.1811066116  1
2019 Stein A, Fowler DM, Hartmann-Petersen R, Lindorff-Larsen K. Biophysical and Mechanistic Models for Disease-Causing Protein Variants. Trends in Biochemical Sciences. PMID 30712981 DOI: 10.1016/J.Tibs.2019.01.003  1
2019 Stein A, Fowler DM, Hartmann-Petersen R, Lindorff-Larsen K. Biophysical and Mechanistic Models for Disease-Causing Protein Variants. Trends in Biochemical Sciences. PMID 30712981 DOI: 10.1016/J.Tibs.2019.01.003  1
2019 Scheller R, Stein A, Nielsen SV, Marin FI, Gerdes AM, Marco MD, Papaleo E, Lindorff-Larsen K, Hartmann-Petersen R. Towards mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations. Human Mutation. PMID 30648773 DOI: 10.1002/humu.23707  1
2019 Scheller R, Stein A, Nielsen SV, Marin FI, Gerdes AM, Marco MD, Papaleo E, Lindorff-Larsen K, Hartmann-Petersen R. Towards mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations. Human Mutation. PMID 30648773 DOI: 10.1002/humu.23707  1
2019 Clausen L, Abildgaard AB, Gersing SK, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Protein stability and degradation in health and disease. Advances in Protein Chemistry and Structural Biology. 114: 61-83. PMID 30635086 DOI: 10.1016/bs.apcsb.2018.09.002  1
2019 Clausen L, Abildgaard AB, Gersing SK, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Protein stability and degradation in health and disease. Advances in Protein Chemistry and Structural Biology. 114: 61-83. PMID 30635086 DOI: 10.1016/bs.apcsb.2018.09.002  1
2018 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. Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space. Cell. 175: 1365-1379.e25. PMID 30445040 DOI: 10.1016/j.cell.2018.10.039  1
2018 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. Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space. Cell. 175: 1365-1379.e25. PMID 30445040 DOI: 10.1016/j.cell.2018.10.039  1
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  1
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  1
2018 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. Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments. Molecular Cell. PMID 30244836 DOI: 10.1016/J.Molcel.2018.08.027  1
2018 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. Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments. Molecular Cell. PMID 30244836 DOI: 10.1016/J.Molcel.2018.08.027  1
2018 Santner P, Martins JMDS, Laursen JS, Behrendt L, Riber L, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel. Biochemistry. 57: 5949-5956. PMID 30230312 DOI: 10.1021/Acs.Biochem.8B00721  1
2018 Santner P, Martins JMDS, Laursen JS, Behrendt L, Riber L, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel. Biochemistry. 57: 5949-5956. PMID 30230312 DOI: 10.1021/Acs.Biochem.8B00721  1
2018 Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. Random mutagenesis analysis of the Influenza A M2 proton channel reveals novel resistance mutants. Biochemistry. PMID 30230310 DOI: 10.1021/Acs.Biochem.8B00722  1
2018 Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. Random mutagenesis analysis of the Influenza A M2 proton channel reveals novel resistance mutants. Biochemistry. PMID 30230310 DOI: 10.1021/Acs.Biochem.8B00722  1
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  1
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  1
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  1
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  1
2018 Kassem MM, Christoffersen LB, Cavalli A, Lindorff-Larsen K. Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts. Scientific Reports. 8: 11112. PMID 30042380 DOI: 10.1038/s41598-018-29357-y  1
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  1
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  1
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  1
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  1
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  1
2018 Kumar GS, Clarkson MW, Kunze MBA, Granata D, Wand AJ, Lindorff-Larsen K, Page R, Peti W. Dynamic activation and regulation of the mitogen-activated protein kinase p38. Proceedings of the National Academy of Sciences of the United States of America. PMID 29666261 DOI: 10.1073/Pnas.1721441115  1
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  1
2018 Johansson KE, Lindorff-Larsen K. Structural heterogeneity and dynamics in protein evolution and design. Current Opinion in Structural Biology. 48: 157-163. PMID 29413956 DOI: 10.1016/j.sbi.2018.01.010  1
2017 Wang Y, Martins JM, Lindorff-Larsen K. Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics. Chemical Science. 8: 6466-6473. PMID 29619200 DOI: 10.1039/c7sc01627a  1
2017 Wang Y, Bugge K, Kragelund BB, Lindorff-Larsen K. Role of protein dynamics in transmembrane receptor signalling. Current Opinion in Structural Biology. 48: 74-82. PMID 29136528 DOI: 10.1016/j.sbi.2017.10.017  1
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  1
2017 Kampmeyer C, Nielsen SV, Clausen L, Stein A, Gerdes AM, Lindorff-Larsen K, Hartmann-Petersen R. Blocking protein quality control to counter hereditary cancers. Genes, Chromosomes & Cancer. PMID 28779490 DOI: 10.1002/gcc.22487  1
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  1
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  1
2017 Hendus-Altenburger R, Lambrughi M, Terkelsen T, Pedersen SF, Papaleo E, Lindorff-Larsen K, Kragelund BB. A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1). Cellular Signalling. 37: 40-51. PMID 28554535 DOI: 10.1016/j.cellsig.2017.05.015  1
2017 Nielsen SV, Stein A, Dinitzen AB, Papaleo E, Tatham MH, Poulsen EG, Kassem MM, Rasmussen LJ, Lindorff-Larsen K, Hartmann-Petersen R. Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations. Plos Genetics. 13: e1006739. PMID 28422960 DOI: 10.1371/journal.pgen.1006739  1
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  1
2017 Phuong TT, Larsen CØ, Røndbjerg T, De Foresta M, Kunze MB, Marek A, Hartvig Løper J, Boyhus LE, Knuhtsen A, Lindorff-Larsen K, Sejer Pedersen D. Diversity-Oriented Peptide Stapling: A Third Generation CuAAC Stapling and Functionalisation Strategy. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 28106305 DOI: 10.1002/Chem.201700128  1
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  1
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  1
2017 Steinocher H, Bugge K, Nikolajsen LF, Lindorff-Larsen K, Brooks A, Kragelund BB. Class I Cytokine Receptors: Towards the Inside Biophysical Journal. 112: 1-1. DOI: 10.1016/J.Bpj.2016.11.947  1
2016 Johansson KE, Johansen NT, Christensen S, Horowitz S, Bardwell JC, Olsen JG, Willemoës M, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T, Winther JR. Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template. Journal of Molecular Biology. PMID 27659562 DOI: 10.1016/J.Jmb.2016.09.013  1
2016 Lambrughi M, De Gioia L, Gervasio FL, Lindorff-Larsen K, Nussinov R, Urani C, Bruschi M, Papaleo E. DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions. Nucleic Acids Research. 44: 9096-9109. PMID 27604871 DOI: 10.1093/Nar/Gkw770  1
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  1
2016 Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? The Febs Journal. 283: 4424-4451. PMID 27350538 DOI: 10.1111/febs.13793  1
2016 Højgaard C, Kofoed C, Espersen R, Johansson KE, Villa M, Willemoës M, Lindorff-Larsen K, Teilum K, Winther JR. A Soluble, Folded Protein Without Charged Amino Acid Residues. Biochemistry. PMID 27307139 DOI: 10.1021/Acs.Biochem.6B00269  1
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  1
2016 Bugge K, Papaleo E, Haxholm GW, Hopper JT, Robinson CV, Olsen JG, Lindorff-Larsen K, Kragelund BB. A combined computational and structural model of the full-length human prolactin receptor. Nature Communications. 7: 11578. PMID 27174498 DOI: 10.1038/ncomms11578  1
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  1
2016 Boomsma W, Nielsen SV, Lindorff-Larsen K, Hartmann-Petersen R, Ellgaard L. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases Peerj. 4. PMID 26966660 DOI: 10.7717/Peerj.1725  1
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  1
2016 Schafer NP, Truong HH, Otzen DE, Lindorff-Larsen K, Wolynes PG. 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. PMID 26858402 DOI: 10.1073/Pnas.1524027113  1
2016 Schafer NP, Truong HH, Otzen DE, Lindorff-Larsen K, Wolynes PG. 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. PMID 26858402 DOI: 10.1073/Pnas.1524027113  1
2016 Tian P, Lindorff-Larsen K, Boomsma W, Jensen MH, Otzen DE. A Monte Carlo Study of the Early Steps of Functional Amyloid Formation. Plos One. 11: e0146096. PMID 26745180 DOI: 10.1371/Journal.Pone.0146096  1
2016 Tian P, Lindorff-Larsen K, Boomsma W, Jensen MH, Otzen DE. A Monte Carlo Study of the Early Steps of Functional Amyloid Formation. Plos One. 11: e0146096. PMID 26745180 DOI: 10.1371/Journal.Pone.0146096  1
2016 Tian P, Lindorff-Larsen K, Boomsma W, Jensen MH, Otzen DE. A monte carlo study of the early steps of functional amyloid formation Plos One. 11. DOI: 10.1371/journal.pone.0146096  1
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  1
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  1
2015 Bugge K, Steinocher H, Brooks AJ, Lindorff-Larsen K, Kragelund BB. Exploiting Hydrophobicity for Efficient Production of Transmembrane Helices for Structure Determination by NMR Spectroscopy. Analytical Chemistry. 87: 9126-31. PMID 26309151 DOI: 10.1021/Acs.Analchem.5B02365  1
2015 Bugge K, Steinocher H, Brooks AJ, Lindorff-Larsen K, Kragelund BB. Exploiting Hydrophobicity for Efficient Production of Transmembrane Helices for Structure Determination by NMR Spectroscopy. Analytical Chemistry. 87: 9126-31. PMID 26309151 DOI: 10.1021/Acs.Analchem.5B02365  1
2015 Mathiassen SG, Larsen IB, Poulsen EG, Madsen CT, Papaleo E, Lindorff-Larsen K, Kragelund BB, Nielsen ML, Kriegenburg F, Hartmann-Petersen R. A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast. The Journal of Biological Chemistry. 290: 21141-53. PMID 26152728 DOI: 10.1074/jbc.M115.662312  1
2015 Mathiassen SG, Larsen IB, Poulsen EG, Madsen CT, Papaleo E, Lindorff-Larsen K, Kragelund BB, Nielsen ML, Kriegenburg F, Hartmann-Petersen R. A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast. The Journal of Biological Chemistry. 290: 21141-53. PMID 26152728 DOI: 10.1074/jbc.M115.662312  1
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  1
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  1
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  1
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  1
2015 Tian P, Boomsma W, Wang Y, Otzen DE, Jensen MH, Lindorff-Larsen K. Structure of a functional amyloid protein subunit computed using sequence variation. Journal of the American Chemical Society. 137: 22-5. PMID 25415595 DOI: 10.1021/Ja5093634  1
2015 Tian P, Boomsma W, Wang Y, Otzen DE, Jensen MH, Lindorff-Larsen K. Structure of a functional amyloid protein subunit computed using sequence variation. Journal of the American Chemical Society. 137: 22-5. PMID 25415595 DOI: 10.1021/Ja5093634  1
2015 Tian P, Boomsma W, Wang Y, Otzen DE, Jensen MH, Lindorff-Larsen K. What does Evolution Tell us about the Structure of a Functional Amyloid Protein Biophysical Journal. 108: 2-7. DOI: 10.1016/J.Bpj.2014.11.1253  1
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  1
2014 Olsson S, Vögeli BR, Cavalli A, Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K, Hamelryck T. Probabilistic Determination of Native State Ensembles of Proteins. Journal of Chemical Theory and Computation. 10: 3484-91. PMID 26588313 DOI: 10.1021/Ct5001236  1
2014 Tian P, Jónsson SÆ, Ferkinghoff-Borg J, Krivov SV, Lindorff-Larsen K, Irbäck A, Boomsma W. Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling Journal of Chemical Theory and Computation. 10: 543-553. PMID 26580031 DOI: 10.1021/Ct400844X  1
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  1
2014 Invernizzi G, Tiberti M, Lambrughi M, Lindorff-Larsen K, Papaleo E. Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops. Plos Computational Biology. 10: e1003744. PMID 25187961 DOI: 10.1371/journal.pcbi.1003744  1
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  1
2014 Tian P, Jónsson S, Ferkinghoff-Borg J, Krivov S, Lindorff-Larsen K, Boomsma W. Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling Biophysical Journal. 106: 640. DOI: 10.1016/J.Bpj.2013.11.3543  1
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  1
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  1
2013 Christensen AS, Linnet TE, Borg M, Boomsma W, Lindorff-Larsen K, Hamelryck T, Jensen JH. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. Plos One. 8: e84123. PMID 24391900 DOI: 10.1371/Journal.Pone.0084123  1
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  1
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  1
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  1
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  1
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  1
2013 Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE. Correction: Systematic validation of protein force fields against experimental data (PLoS ONE) Plos One. 8. DOI: 10.1371/Annotation/8301B5D4-1Ba3-40E7-8Fcd-3E169B967044  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2010 Jensen MØ, Borhani DW, Lindorff-Larsen K, Maragakis P, Jogini V, Eastwood MP, Dror RO, Shaw DE. Principles of conduction and hydrophobic gating in K+ channels. Proceedings of the National Academy of Sciences of the United States of America. 107: 5833-8. PMID 20231479 DOI: 10.1073/Pnas.0911691107  1
2010 Jensen MØ, Borhani DW, Lindorff-Larsen K, Maragakis P, Jogini V, Eastwood MP, Dror RO, Shaw DE. Principles of conduction and hydrophobic gating in K+ channels. Proceedings of the National Academy of Sciences of the United States of America. 107: 5833-8. PMID 20231479 DOI: 10.1073/Pnas.0911691107  1
2010 Jensen M, Borhani DW, Lindorff-Larsen K, Dror RO, Shaw DE. Reply to Domene and Furini: Distinguishing knock-on and vacancy diffusion mechanisms Proceedings of the National Academy of Sciences of the United States of America. 107: E129. DOI: 10.1073/Pnas.1008197107  1
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  1
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  1
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  1
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  1
2009 Lindorff-Larsen K, Ferkinghoff-Borg J. Similarity measures for protein ensembles. Plos One. 4: e4203. PMID 19145244 DOI: 10.1371/journal.pone.0004203  1
2009 Lindorff-Larsen K, Ferkinghoff-Borg J. Similarity measures for protein ensembles. Plos One. 4: e4203. PMID 19145244 DOI: 10.1371/journal.pone.0004203  1
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  1
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  1
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  1
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  1
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  1
2007 Modig K, Jürgensen VW, Lindorff-Larsen K, Fieber W, Bohr HG, Poulsen FM. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis. Febs Letters. 581: 4965-71. PMID 17910956 DOI: 10.1016/j.febslet.2007.09.027  1
2007 Modig K, Jürgensen VW, Lindorff-Larsen K, Fieber W, Bohr HG, Poulsen FM. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis. Febs Letters. 581: 4965-71. PMID 17910956 DOI: 10.1016/j.febslet.2007.09.027  1
2007 Geierhaas CD, Nickson AA, Lindorff-Larsen K, Clarke J, Vendruscolo M. BPPred: a Web-based computational tool for predicting biophysical parameters of proteins. Protein Science : a Publication of the Protein Society. 16: 125-34. PMID 17123959 DOI: 10.1110/Ps.062383807  1
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  1
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  1
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  1
2006 Chandran V, Stollar EJ, Lindorff-Larsen K, Harper JF, Chazin WJ, Dobson CM, Luisi BF, Christodoulou J. Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition. Journal of Molecular Biology. 357: 400-10. PMID 16430916 DOI: 10.1016/J.Jmb.2005.11.093  1
2005 Paci E, Lindorff-Larsen K, Dobson CM, Karplus M, Vendruscolo M. Transition state contact orders correlate with protein folding rates. Journal of Molecular Biology. 352: 495-500. PMID 16120445 DOI: 10.1016/J.Jmb.2005.06.081  1
2005 Kristjansdottir S, Lindorff-Larsen K, Fieber W, Dobson CM, Vendruscolo M, Poulsen FM. Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies. Journal of Molecular Biology. 347: 1053-62. PMID 15784263 DOI: 10.1016/J.Jmb.2005.01.009  1
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  1
2004 Paci E, Friel CT, Lindorff-Larsen K, Radford SE, Karplus M, Vendruscolo M. Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints. Proteins. 54: 513-25. PMID 14747999 DOI: 10.1002/Prot.10595  1
2001 Lindorff-Larsen K, Lerche MH, Poulsen FM, Roepstorff P, Winther JR. Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification. The Journal of Biological Chemistry. 276: 33547-53. PMID 11435437 DOI: 10.1074/jbc.M104841200  1
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