1zbj Citations

Inferential structure determination.

Science 309 303-6 (2005)
Cited: 131 times
EuropePMC logo PMID: 16002620


Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.

Reviews citing this publication (29)

  1. Using simulation to interpret experimental data in terms of protein conformational ensembles. Allison JR. Curr. Opin. Struct. Biol. 43 79-87 (2017)
  2. Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates. Linser R. Solid State Nucl Magn Reson 87 45-53 (2017)
  3. Principles of protein structural ensemble determination. Bonomi M, Heller GT, Camilloni C, Vendruscolo M. Curr. Opin. Struct. Biol. 42 106-116 (2017)
  4. A community resource of experimental data for NMR / X-ray crystal structure pairs. Everett JK, Tejero R, Murthy SB, Acton TB, Aramini JM, Baran MC, Benach J, Cort JR, Eletsky A, Forouhar F, Guan R, Kuzin AP, Lee HW, Liu G, Mani R, Mao B, Mills JL, Montelione AF, Pederson K, Powers R, Ramelot T, Rossi P, Seetharaman J, Snyder D, Swapna GV, Vorobiev SM, Wu Y, Xiao R, Yang Y, Arrowsmith CH, Hunt JF, Kennedy MA, Prestegard JH, Szyperski T, Tong L, Montelione GT. Protein Sci. 25 30-45 (2016)
  5. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Curr. Opin. Struct. Biol. 40 163-185 (2016)
  6. Deriving Structural Information from Experimentally Measured Data on Biomolecules. van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Angew. Chem. Int. Ed. Engl. 55 15990-16010 (2016)
  7. Assembling the pieces of macromolecular complexes: Hybrid structural biology approaches. Politis A, Borysik AJ. Proteomics 15 2792-2803 (2015)
  8. Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. Flot JF, Marie-Nelly H, Koszul R. FEBS Lett. 589 2966-2974 (2015)
  9. Integrative, dynamic structural biology at atomic resolution--it's about time. van den Bedem H, Fraser JS. Nat. Methods 12 307-318 (2015)
  10. The importance of dynamics in integrative modeling of supramolecular assemblies. Tamò GE, Abriata LA, Dal Peraro M. Curr. Opin. Struct. Biol. 31 28-34 (2015)
  11. Hybrid methods for macromolecular structure determination: experiment with expectations. Schröder GF. Curr. Opin. Struct. Biol. 31 20-27 (2015)
  12. An overview of tools for the validation of protein NMR structures. Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A. J. Biomol. NMR 58 259-285 (2014)
  13. Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Purdy MD, Bennett BC, McIntire WE, Khan AK, Kasson PM, Yeager M. Curr. Opin. Struct. Biol. 27 138-148 (2014)
  14. Uncertainty in integrative structural modeling. Schneidman-Duhovny D, Pellarin R, Sali A. Curr. Opin. Struct. Biol. 28 96-104 (2014)
  15. The dynamic duo: combining NMR and small angle scattering in structural biology. Hennig J, Sattler M. Protein Sci. 23 669-682 (2014)
  16. Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs. Vögeli B, Orts J, Strotz D, Chi C, Minges M, Wälti MA, Güntert P, Riek R. J. Magn. Reson. 241 53-59 (2014)
  17. Combining experiments and simulations using the maximum entropy principle. Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K. PLoS Comput. Biol. 10 e1003406 (2014)
  18. The nuclear Overhauser effect from a quantitative perspective. Vögeli B. Prog Nucl Magn Reson Spectrosc 78 1-46 (2014)
  19. Protein modeling: what happened to the "protein structure gap"? Schwede T. Structure 21 1531-1540 (2013)
  20. Solid state NMR and protein-protein interactions in membranes. Miao Y, Cross TA. Curr. Opin. Struct. Biol. 23 919-928 (2013)
  21. Advances in automated NMR protein structure determination. Guerry P, Herrmann T. Q. Rev. Biophys. 44 257-309 (2011)
  22. Constructing ensembles for intrinsically disordered proteins. Fisher CK, Stultz CM. Curr. Opin. Struct. Biol. 21 426-431 (2011)
  23. Visualization of macromolecular structures. O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ. Nat. Methods 7 S42-55 (2010)
  24. Structure-oriented methods for protein NMR data analysis. Bermejo GA, Llinás M. Prog Nucl Magn Reson Spectrosc 56 311-328 (2010)
  25. Probabilistic models and machine learning in structural bioinformatics. Hamelryck T. Stat Methods Med Res 18 505-526 (2009)
  26. Conformational averaging in structural biology: issues, challenges and computational solutions. Kruschel D, Zagrovic B. Mol Biosyst 5 1606-1616 (2009)
  27. Integrating diverse data for structure determination of macromolecular assemblies. Alber F, Förster F, Korkin D, Topf M, Sali A. Annu. Rev. Biochem. 77 443-477 (2008)
  28. Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings. Bouvignies G, Markwick PR, Blackledge M. Chemphyschem 8 1901-1909 (2007)
  29. The molecular sociology of the cell. Robinson CV, Sali A, Baumeister W. Nature 450 973-982 (2007)

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  1. Structure of the human voltage-dependent anion channel. Bayrhuber M, Meins T, Habeck M, Becker S, Giller K, Villinger S, Vonrhein C, Griesinger C, Zweckstetter M, Zeth K. Proc. Natl. Acad. Sci. U.S.A. 105 15370-15375 (2008)
  2. High-resolution structure prediction and the crystallographic phase problem. Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. Nature 450 259-264 (2007)
  3. White matter pathology isolates the hippocampal formation in Alzheimer's disease. Salat DH, Tuch DS, van der Kouwe AJ, Greve DN, Pappu V, Lee SY, Hevelone ND, Zaleta AK, Growdon JH, Corkin S, Fischl B, Rosas HD. Neurobiol. Aging 31 244-256 (2010)
  4. other Outcome of the first electron microscopy validation task force meeting. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Structure 20 205-214 (2012)
  5. The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. Richter B, Gsponer J, Várnai P, Salvatella X, Vendruscolo M. J. Biomol. NMR 37 117-135 (2007)
  6. Biochemistry. Integrative structural biology. Ward AB, Sali A, Wilson IA. Science 339 913-915 (2013)
  7. Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Cell 158 1123-1135 (2014)
  8. Bayesian inference of spatial organizations of chromosomes. Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. PLoS Comput. Biol. 9 e1002893 (2013)
  9. Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M. BMC Bioinformatics 12 414 (2011)
  10. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. Proteins 69 449-465 (2007)
  11. Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals. Shahid SA, Bardiaux B, Franks WT, Krabben L, Habeck M, van Rossum BJ, Linke D. Nat. Methods 9 1212-1217 (2012)
  12. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. Mol. Cell Proteomics 13 2927-2943 (2014)
  13. Weighting of experimental evidence in macromolecular structure determination. Habeck M, Rieping W, Nilges M. Proc. Natl. Acad. Sci. U.S.A. 103 1756-1761 (2006)
  14. Structural biology by NMR: structure, dynamics, and interactions. Markwick PR, Malliavin T, Nilges M. PLoS Comput. Biol. 4 e1000168 (2008)
  15. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Structure 22 1239-1251 (2014)
  16. High-quality genome (re)assembly using chromosomal contact data. Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R. Nat Commun 5 5695 (2014)
  17. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Structure 23 1156-1167 (2015)
  18. A strategy for dissecting the architectures of native macromolecular assemblies. Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. Nat. Methods 12 1135-1138 (2015)
  19. Structure validation of the Josephin domain of ataxin-3: conclusive evidence for an open conformation. Nicastro G, Habeck M, Masino L, Svergun DI, Pastore A. J. Biomol. NMR 36 267-277 (2006)
  20. ISD: a software package for Bayesian NMR structure calculation. Rieping W, Nilges M, Habeck M. Bioinformatics 24 1104-1105 (2008)
  21. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A. Proc. Natl. Acad. Sci. U.S.A. 109 18821-18826 (2012)
  22. Accurate NMR structures through minimization of an extended hybrid energy. Nilges M, Bernard A, Bardiaux B, Malliavin T, Habeck M, Rieping W. Structure 16 1305-1312 (2008)
  23. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. MacCallum JL, Perez A, Dill KA. Proc. Natl. Acad. Sci. U.S.A. 112 6985-6990 (2015)
  24. High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations. Zeng J, Boyles J, Tripathy C, Wang L, Yan A, Zhou P, Donald BR. J. Biomol. NMR 45 265-281 (2009)
  25. Metainference: A Bayesian inference method for heterogeneous systems. Bonomi M, Camilloni C, Cavalli A, Vendruscolo M. Sci Adv 2 e1501177 (2016)
  26. Molecular architecture of the yeast Mediator complex. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Elife 4 (2015)
  27. Flexible backbone sampling methods to model and design protein alternative conformations. Ollikainen N, Smith CA, Fraser JS, Kortemme T. Meth. Enzymol. 523 61-85 (2013)
  28. Accurate protein structure modeling using sparse NMR data and homologous structure information. Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT, Baker D. Proc. Natl. Acad. Sci. U.S.A. 109 9875-9880 (2012)
  29. Inference of structure ensembles of flexible biomolecules from sparse, averaged data. Olsson S, Frellsen J, Boomsma W, Mardia KV, Hamelryck T. PLoS ONE 8 e79439 (2013)
  30. Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics. Chen PC, Hub JS. Biophys. J. 108 2573-2584 (2015)
  31. Bayesian energy landscape tilting: towards concordant models of molecular ensembles. Beauchamp KA, Pande VS, Das R. Biophys. J. 106 1381-1390 (2014)
  32. Similarity measures for protein ensembles. Lindorff-Larsen K, Ferkinghoff-Borg J. PLoS ONE 4 e4203 (2009)
  33. Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. Lezon TR, Bahar I. PLoS Comput. Biol. 6 e1000816 (2010)
  34. Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints. Donald BR, Martin J. Prog Nucl Magn Reson Spectrosc 55 101-127 (2009)
  35. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. Stovgaard K, Andreetta C, Ferkinghoff-Borg J, Hamelryck T. BMC Bioinformatics 11 429 (2010)
  36. Inferential modeling of 3D chromatin structure. Wang S, Xu J, Zeng J. Nucleic Acids Res. 43 e54 (2015)
  37. Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints. Lin M, Lu HM, Chen R, Liang J. J Chem Phys 129 094101 (2008)
  38. Finding Our Way in the Dark Proteome. Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. J. Am. Chem. Soc. 138 9730-9742 (2016)
  39. Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles. Buchner L, Güntert P. Structure 23 425-434 (2015)
  40. Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures. Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE. Proteins 79 1525-1537 (2011)
  41. Structure of the inhibitor W7 bound to the regulatory domain of cardiac troponin C. Hoffman RM, Sykes BD. Biochemistry 48 5541-5552 (2009)
  42. A Bayesian statistics approach to multiscale coarse graining. Liu P, Shi Q, Daumé H, Voth GA. J Chem Phys 129 214114 (2008)
  43. Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants. Habeck M, Rieping W, Nilges M. J. Magn. Reson. 177 160-165 (2005)
  44. 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. 111 13852-13857 (2014)
  45. COCO: a simple tool to enrich the representation of conformational variability in NMR structures. Laughton CA, Orozco M, Vranken W. Proteins 75 206-216 (2009)
  46. Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5. Garza-Garcia A, Esposito D, Rieping W, Harris R, Briggs C, Brown MH, Driscoll PC. J. Mol. Biol. 378 129-144 (2008)
  47. A unifying probabilistic framework for analyzing residual dipolar couplings. Habeck M, Nilges M, Rieping W. J. Biomol. NMR 40 135-144 (2008)
  48. Bayesian inference applied to macromolecular structure determination. Habeck M, Nilges M, Rieping W. Phys Rev E Stat Nonlin Soft Matter Phys 72 031912 (2005)
  49. Bayesian inference of protein ensembles from SAXS data. Antonov LD, Olsson S, Boomsma W, Hamelryck T. Phys Chem Chem Phys 18 5832-5838 (2016)
  50. 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 8 e84123 (2013)
  51. Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. Cossio P, Hummer G. J. Struct. Biol. 184 427-437 (2013)
  52. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data. Zeng J, Zhou P, Donald BR. J. Biomol. NMR 50 371-395 (2011)
  53. A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. Wang L, Mettu RR, Donald BR. J. Comput. Biol. 13 1267-1288 (2006)
  54. Error distribution derived NOE distance restraints. Nilges M, Habeck M, O'Donoghue SI, Rieping W. Proteins 64 652-664 (2006)
  55. Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics. Bonomi M, Camilloni C, Vendruscolo M. Sci Rep 6 31232 (2016)
  56. Mixture models for protein structure ensembles. Hirsch M, Habeck M. Bioinformatics 24 2184-2192 (2008)
  57. An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. Hung LH, Samudrala R. J. Biomol. NMR 36 189-198 (2006)
  58. Inferential backbone assignment for sparse data. Vitek O, Bailey-Kellogg C, Craig B, Vitek J. J. Biomol. NMR 35 187-208 (2006)
  59. A global analysis of NMR distance constraints from the PDB. Vranken W. J. Biomol. NMR 39 303-314 (2007)
  60. Bayesian ensemble refinement by replica simulations and reweighting. Hummer G, Köfinger J. J Chem Phys 143 243150 (2015)
  61. Bayesian inference of conformational state populations from computational models and sparse experimental observables. Voelz VA, Zhou G. J Comput Chem 35 2215-2224 (2014)
  62. Evolutionary Pareto-optimization of stably folding peptides. Gronwald W, Hohm T, Hoffmann D. BMC Bioinformatics 9 109 (2008)
  63. Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data. Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. Mol. Cell Proteomics 13 2812-2823 (2014)
  64. An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D. Genome Res. 26 1697-1709 (2016)
  65. Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling. Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J. Mol. Cell Proteomics 15 2730-2743 (2016)
  66. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. J. Struct. Biol. 194 303-310 (2016)
  67. A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm. Brunner K, Gronwald W, Trenner JM, Neidig KP, Kalbitzer HR. BMC Struct. Biol. 6 14 (2006)
  68. Improved in-cell structure determination of proteins at near-physiological concentration. Ikeya T, Hanashima T, Hosoya S, Shimazaki M, Ikeda S, Mishima M, Güntert P, Ito Y. Sci Rep 6 38312 (2016)
  69. Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli. Habenstein B, Loquet A, Hwang S, Giller K, Vasa SK, Becker S, Habeck M, Lange A. Angew. Chem. Int. Ed. Engl. 54 11691-11695 (2015)
  70. Structure and evolution of N-domains in AAA metalloproteases. Scharfenberg F, Serek-Heuberger J, Coles M, Hartmann MD, Habeck M, Martin J, Lupas AN, Alva V. J. Mol. Biol. 427 910-923 (2015)
  71. The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction. Snyder DA, Grullon J, Huang YJ, Tejero R, Montelione GT. Proteins 82 Suppl 2 219-230 (2014)
  72. Statistical characterization of protein ensembles. Rother D, Sapiro G, Pande V. IEEE/ACM Trans Comput Biol Bioinform 5 42-55 (2008)
  73. Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data. Carstens S, Nilges M, Habeck M. PLoS Comput. Biol. 12 e1005292 (2016)
  74. Blind protein structure prediction using accelerated free-energy simulations. Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA. Sci Adv 2 e1601274 (2016)
  75. A critical assessment of methods to recover information from averaged data. Ravera E, Sgheri L, Parigi G, Luchinat C. Phys Chem Chem Phys 18 5686-5701 (2016)
  76. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. J. Biol. Chem. 290 30390-30405 (2015)
  77. Bayesian inference of protein structure from chemical shift data. Bratholm LA, Christensen AS, Hamelryck T, Jensen JH. PeerJ 3 e861 (2015)
  78. Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings. Sanchez-Martinez M, Crehuet R. Phys Chem Chem Phys 16 26030-26039 (2014)
  79. Visualising intrinsic disorder and conformational variation in protein ensembles. Heinrich J, Krone M, O'Donoghue SI, Weiskopf D. Faraday Discuss. 169 179-193 (2014)
  80. A simple probabilistic model of multibody interactions in proteins. Johansson KE, Hamelryck T. Proteins 81 1340-1350 (2013)
  81. The impact of entropy on the spatial organization of synaptonemal complexes within the cell nucleus. Fritsche M, Reinholdt LG, Lessard M, Handel MA, Bewersdorf J, Heermann DW. PLoS ONE 7 e36282 (2012)
  82. The effects of rigid motions on elastic network model force constants. Lezon TR. Proteins 80 1133-1142 (2012)
  83. A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. Zeng J, Roberts KE, Zhou P, Donald BR. J. Comput. Biol. 18 1661-1679 (2011)
  84. CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data. Angyán AF, Szappanos B, Perczel A, Gáspári Z. BMC Struct. Biol. 10 39 (2010)
  85. In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. Müller CL, Sbalzarini IF, van Gunsteren WF, Zagrović B, Hünenberger PH. J Chem Phys 130 214904 (2009)
  86. Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides. Reppert M, Roy AR, Tempkin JO, Dinner AR, Tokmakoff A. J Phys Chem B 120 11395-11404 (2016)
  87. The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry. Matthew Allen Bullock J, Schwab J, Thalassinos K, Topf M. Mol. Cell Proteomics 15 2491-2500 (2016)
  88. Bayesian weighting of statistical potentials in NMR structure calculation. Mechelke M, Habeck M. PLoS ONE 9 e100197 (2014)
  89. 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 82 288-299 (2014)
  90. Inferential NMR/X-ray-based structure determination of a dibenzo[a,d]cycloheptenone inhibitor-p38α MAP kinase complex in solution. Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C, Habeck M. Angew. Chem. Int. Ed. Engl. 51 2359-2362 (2012)
  91. NMR structural inference of symmetric homo-oligomers. Chandola H, Yan AK, Potluri S, Donald BR, Bailey-Kellogg C. J. Comput. Biol. 18 1757-1775 (2011)
  92. Protein structure calculation with data imputation: the use of substitute restraints. Cano C, Brunner K, Baskaran K, Elsner R, Munte CE, Kalbitzer HR. J. Biomol. NMR 45 397-411 (2009)
  93. Sequential Monte Carlo scheme for Bayesian estimation in the presence of data outliers. Huang L, Lai YC. Phys Rev E Stat Nonlin Soft Matter Phys 75 056705 (2007)
  94. NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin. LeMaster DM, Anderson JS, Wang L, Guo Y, Li H, Hernández G. BMC Struct. Biol. 7 81 (2007)
  95. Probabilistic determination of probe locations from distance data. Xu XP, Slaughter BD, Volkmann N. J. Struct. Biol. 184 75-82 (2013)
  96. MOTOR: model assisted software for NMR structure determination. Schieborr U, Sreeramulu S, Elshorst B, Maurer M, Saxena K, Stehle T, Kudlinzki D, Gande SL, Schwalbe H. Proteins 81 2007-2022 (2013)
  97. The adaptor protein CIN85 assembles intracellular signaling clusters for B cell activation. Kühn J, Wong LE, Pirkuliyeva S, Schulz K, Schwiegk C, Fünfgeld KG, Keppler S, Batista FD, Urlaub H, Habeck M, Becker S, Griesinger C, Wienands J. Sci Signal 9 ra66 (2016)
  98. Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps. Habeck M. Front Mol Biosci 4 15 (2017)
  99. Protein structure refinement using a quantum mechanics-based chemical shielding predictor. Bratholm LA, Jensen JH. Chem Sci 8 2061-2072 (2017)
  100. Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide. Löhr T, Jussupow A, Camilloni C. J Chem Phys 146 165102 (2017)
  101. Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations. Arbona JM, Herbert S, Fabre E, Zimmer C. Genome Biol. 18 81 (2017)
  102. Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics. Shevchuk R, Hub JS. PLoS Comput. Biol. 13 e1005800 (2017)

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