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Items: 31

1.

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 Sep 6. doi: 10.1021/acs.jpcb.8b06335. [Epub ahead of print]

PMID:
30141937
2.

Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo.

Kurut A, Fonseca R, Boomsma W.

J Phys Chem B. 2018 Jan 25;122(3):1195-1204. doi: 10.1021/acs.jpcb.7b11426. Epub 2018 Jan 5.

PMID:
29260565
3.

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.

4.

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases.

Boomsma W, Nielsen SV, Lindorff-Larsen K, Hartmann-Petersen R, Ellgaard L.

PeerJ. 2016 Feb 25;4:e1725. doi: 10.7717/peerj.1725. eCollection 2016.

5.

Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides.

Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard L.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3227-32. doi: 10.1073/pnas.1525790113. Epub 2016 Mar 8.

6.

A Monte Carlo Study of the Early Steps of Functional Amyloid Formation.

Tian P, Lindorff-Larsen K, Boomsma W, Jensen MH, Otzen DE.

PLoS One. 2016 Jan 8;11(1):e0146096. doi: 10.1371/journal.pone.0146096. eCollection 2016.

7.

Bayesian inference of protein ensembles from SAXS data.

Antonov LD, Olsson S, Boomsma W, Hamelryck T.

Phys Chem Chem Phys. 2016 Feb 17;18(8):5832-8. doi: 10.1039/c5cp04886a.

PMID:
26548662
8.

ENCORE: Software for Quantitative Ensemble Comparison.

Tiberti M, Papaleo E, Bengtsen T, Boomsma W, Lindorff-Larsen K.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004415. doi: 10.1371/journal.pcbi.1004415. eCollection 2015 Oct.

9.

Comparing molecular dynamics force fields in the essential subspace.

Martín-García F, Papaleo E, Gomez-Puertas P, Boomsma W, Lindorff-Larsen K.

PLoS One. 2015 Mar 26;10(3):e0121114. doi: 10.1371/journal.pone.0121114. eCollection 2015.

10.

Structure of a functional amyloid protein subunit computed using sequence variation.

Tian P, Boomsma W, Wang Y, Otzen DE, Jensen MH, Lindorff-Larsen K.

J Am Chem Soc. 2015 Jan 14;137(1):22-5. doi: 10.1021/ja5093634. Epub 2014 Dec 22.

PMID:
25415595
11.

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

Boomsma W, Tian P, Frellsen J, Ferkinghoff-Borg J, Hamelryck T, Lindorff-Larsen K, Vendruscolo M.

Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13852-7. doi: 10.1073/pnas.1404948111. Epub 2014 Sep 5.

12.

Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I.

Petrlova J, Bhattacherjee A, Boomsma W, Wallin S, Lagerstedt JO, Irbäck A.

Protein Sci. 2014 Nov;23(11):1559-71. doi: 10.1002/pro.2534. Epub 2014 Aug 23.

13.

Probabilistic Determination of Native State Ensembles of Proteins.

Olsson S, Vögeli BR, Cavalli A, Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K, Hamelryck T.

J Chem Theory Comput. 2014 Aug 12;10(8):3484-91. doi: 10.1021/ct5001236. Epub 2014 Jun 30.

PMID:
26588313
14.

Combining experiments and simulations using the maximum entropy principle.

Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K.

PLoS Comput Biol. 2014 Feb 20;10(2):e1003406. doi: 10.1371/journal.pcbi.1003406. eCollection 2014 Feb. Review.

15.

Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling.

Tian P, Jónsson SÆ, Ferkinghoff-Borg J, Krivov SV, Lindorff-Larsen K, Irbäck A, Boomsma W.

J Chem Theory Comput. 2014 Feb 11;10(2):543-53. doi: 10.1021/ct400844x. Epub 2014 Jan 28.

PMID:
26580031
16.

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

Christensen AS, Linnet TE, Borg M, Boomsma W, Lindorff-Larsen K, Hamelryck T, Jensen JH.

PLoS One. 2013 Dec 31;8(12):e84123. doi: 10.1371/journal.pone.0084123. eCollection 2013.

17.

Inference of structure ensembles of flexible biomolecules from sparse, averaged data.

Olsson S, Frellsen J, Boomsma W, Mardia KV, Hamelryck T.

PLoS One. 2013 Nov 7;8(11):e79439. doi: 10.1371/journal.pone.0079439. eCollection 2013.

18.

Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.

Valentin JB, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J, Frellsen J, Mardia KV, Tian P, Hamelryck T.

Proteins. 2014 Feb;82(2):288-99. doi: 10.1002/prot.24386. Epub 2013 Oct 17.

PMID:
23934827
19.

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

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, Ferkinghoff-Borg J, Hamelryck T.

J Comput Chem. 2013 Jul 15;34(19):1697-705. doi: 10.1002/jcc.23292. Epub 2013 Apr 26.

PMID:
23619610
20.

A sticky cage can slow down folding.

Boomsma W, Lindorff-Larsen K.

Biophys J. 2013 Mar 5;104(5):964-5. doi: 10.1016/j.bpj.2013.01.036. No abstract available.

21.

An efficient null model for conformational fluctuations in proteins.

Harder T, Borg M, Bottaro S, Boomsma W, Olsson S, Ferkinghoff-Borg J, Hamelryck T.

Structure. 2012 Jun 6;20(6):1028-39. doi: 10.1016/j.str.2012.03.020. Epub 2012 May 10.

22.

Subtle Monte Carlo Updates in Dense Molecular Systems.

Bottaro S, Boomsma W, E Johansson K, Andreetta C, Hamelryck T, Ferkinghoff-Borg J.

J Chem Theory Comput. 2012 Feb 14;8(2):695-702. doi: 10.1021/ct200641m. Epub 2012 Jan 18.

PMID:
26596617
23.

Fast large-scale clustering of protein structures using Gauss integrals.

Harder T, Borg M, Boomsma W, Røgen P, Hamelryck T.

Bioinformatics. 2012 Feb 15;28(4):510-5. doi: 10.1093/bioinformatics/btr692. Epub 2011 Dec 22.

PMID:
22199383
24.

Generative probabilistic models extend the scope of inferential structure determination.

Olsson S, Boomsma W, Frellsen J, Bottaro S, Harder T, Ferkinghoff-Borg J, Hamelryck T.

J Magn Reson. 2011 Dec;213(1):182-6. doi: 10.1016/j.jmr.2011.08.039. Epub 2011 Sep 6.

PMID:
21993764
25.

Potentials of mean force for protein structure prediction vindicated, formalized and generalized.

Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J.

PLoS One. 2010 Nov 10;5(11):e13714. doi: 10.1371/journal.pone.0013714.

26.

Beyond rotamers: a generative, probabilistic model of side chains in proteins.

Harder T, Boomsma W, Paluszewski M, Frellsen J, Johansson KE, Hamelryck T.

BMC Bioinformatics. 2010 Jun 5;11:306. doi: 10.1186/1471-2105-11-306.

27.

Statistical assignment of DNA sequences using Bayesian phylogenetics.

Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R.

Syst Biol. 2008 Oct;57(5):750-7. doi: 10.1080/10635150802422316.

PMID:
18853361
28.

Fast phylogenetic DNA barcoding.

Munch K, Boomsma W, Willerslev E, Nielsen R.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3997-4002. doi: 10.1098/rstb.2008.0169.

29.

A generative, probabilistic model of local protein structure.

Boomsma W, Mardia KV, Taylor CC, Ferkinghoff-Borg J, Krogh A, Hamelryck T.

Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8932-7. doi: 10.1073/pnas.0801715105. Epub 2008 Jun 25.

30.

Ancient biomolecules from deep ice cores reveal a forested southern Greenland.

Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, Johnsen S, Steffensen JP, Bennike O, Schwenninger JL, Nathan R, Armitage S, de Hoog CJ, Alfimov V, Christl M, Beer J, Muscheler R, Barker J, Sharp M, Penkman KE, Haile J, Taberlet P, Gilbert MT, Casoli A, Campani E, Collins MJ.

Science. 2007 Jul 6;317(5834):111-4.

31.

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