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Wouter Boomsma - Publications

Affiliations: 
DTU Elektro Technical University of Denmark, Kongens Lyngby, Denmark 
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33 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
2019 Hendus-Altenburger R, Fernandes CB, Bugge K, Kunze MBA, Boomsma W, Kragelund BB. Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range. Journal of Biomolecular Nmr. 73: 713-725. PMID 31598803 DOI: 10.1007/S10858-019-00283-Z  0.347
2019 Prestel A, Wichmann N, Martins JM, Marabini R, Kassem N, Broendum SS, Otterlei M, Nielsen O, Willemoës M, Ploug M, Boomsma W, Kragelund BB. The PCNA interaction motifs revisited: thinking outside the PIP-box Cellular and Molecular Life Sciences. 76: 4923-4943. PMID 31134302 DOI: 10.1007/S00018-019-03150-0  0.304
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  0.416
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  0.464
2018 Kurut A, Fonseca R, Boomsma W. Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo. Journal of Physical Chemistry B. 122: 1195-1204. PMID 29260565 DOI: 10.1021/Acs.Jpcb.7B11426  0.388
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  0.465
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  0.333
2016 Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard L. Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides. Proceedings of the National Academy of Sciences of the United States of America. PMID 26957604 DOI: 10.1073/Pnas.1525790113  0.326
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  0.369
2015 Antonov LD, Olsson S, Boomsma W, Hamelryck T. Bayesian inference of protein ensembles from SAXS data. Physical Chemistry Chemical Physics : Pccp. PMID 26548662 DOI: 10.1039/C5Cp04886A  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  0.488
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  0.418
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  0.438
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  0.457
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  0.398
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  0.34
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  0.489
2014 Petrlova J, Bhattacherjee A, Boomsma W, Wallin S, Lagerstedt JO, Irbäck A. Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I. Protein Science : a Publication of the Protein Society. 23: 1559-71. PMID 25131953 DOI: 10.1002/Pro.2534  0.349
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  0.418
2014 Valentin JB, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J, Frellsen J, Mardia KV, Tian P, Hamelryck T. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method. Proteins. 82: 288-99. PMID 23934827 DOI: 10.1002/Prot.24386  0.456
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  0.366
2013 Olsson S, Frellsen J, Boomsma W, Mardia KV, Hamelryck T. Inference of structure ensembles of flexible biomolecules from sparse, averaged data. Plos One. 8: e79439. PMID 24244505 DOI: 10.1371/Journal.Pone.0079439  0.414
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  0.455
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  0.422
2012 Bottaro S, Boomsma W, E Johansson K, Andreetta C, Hamelryck T, Ferkinghoff-Borg J. Subtle Monte Carlo Updates in Dense Molecular Systems. Journal of Chemical Theory and Computation. 8: 695-702. PMID 26596617 DOI: 10.1021/Ct200641M  0.44
2012 Harder T, Borg M, Bottaro S, Boomsma W, Olsson S, Ferkinghoff-Borg J, Hamelryck T. An efficient null model for conformational fluctuations in proteins. Structure (London, England : 1993). 20: 1028-39. PMID 22578545 DOI: 10.1016/J.Str.2012.03.020  0.468
2012 Harder T, Borg M, Boomsma W, Røgen P, Hamelryck T. Fast large-scale clustering of protein structures using Gauss integrals. Bioinformatics (Oxford, England). 28: 510-5. PMID 22199383 DOI: 10.1093/Bioinformatics/Btr692  0.345
2011 Olsson S, Boomsma W, Frellsen J, Bottaro S, Harder T, Ferkinghoff-Borg J, Hamelryck T. Generative probabilistic models extend the scope of inferential structure determination. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 213: 182-6. PMID 21993764 DOI: 10.1016/J.Jmr.2011.08.039  0.432
2010 Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J. Potentials of mean force for protein structure prediction vindicated, formalized and generalized. Plos One. 5: e13714. PMID 21103041 DOI: 10.1371/Journal.Pone.0013714  0.484
2010 Harder T, Boomsma W, Paluszewski M, Frellsen J, Johansson KE, Hamelryck T. Beyond rotamers: a generative, probabilistic model of side chains in proteins. Bmc Bioinformatics. 11: 306. PMID 20525384 DOI: 10.1186/1471-2105-11-306  0.405
2008 Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R. Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology. 57: 750-7. PMID 18853361 DOI: 10.1080/10635150802422316  0.313
2008 Boomsma W, Mardia KV, Taylor CC, Ferkinghoff-Borg J, Krogh A, Hamelryck T. A generative, probabilistic model of local protein structure. Proceedings of the National Academy of Sciences of the United States of America. 105: 8932-7. PMID 18579771 DOI: 10.1073/Pnas.0801715105  0.487
2005 Boomsma W, Hamelryck T. Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. Bmc Bioinformatics. 6: 159. PMID 15985178 DOI: 10.1186/1471-2105-6-159  0.405
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