| Year |
Citation |
Score |
| 2020 |
Grønbæk C, Hamelryck T, Røgen P. GISA: using Gauss Integrals to identify rare conformations in protein structures. Peerj. 8: e9159. PMID 32566389 DOI: 10.7717/Peerj.9159 |
0.508 |
|
| 2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000research. 9. PMID 32566135 DOI: 10.12688/F1000Research.20559.1 |
0.367 |
|
| 2019 |
Moreta LS, Al-Sibahi AS, Theobald D, Bullock W, Rommes BN, Manoukian A, Hamelryck T. A Probabilistic Programming Approach to Protein Structure Superposition. Proceedings of the ... Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology : Cibcb. Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology. 2019. PMID 34661202 DOI: 10.1109/cibcb.2019.8791469 |
0.717 |
|
| 2018 |
Postic G, Hamelryck T, Chomilier J, Stratmann D. MyPMFs: a simple tool for creating statistical potentials to assess protein structural models. Biochimie. PMID 29857183 DOI: 10.1016/j.biochi.2018.05.013 |
0.388 |
|
| 2017 |
Golden M, Garcia-Portugues E, Sørensen M, Mardia KV, Hamelryck T, Hein J. A generative angular model of protein structure evolution. Molecular Biology and Evolution. PMID 28453724 DOI: 10.1093/Molbev/Msx137 |
0.46 |
|
| 2017 |
García-Portugués E, Sørensen M, Mardia KV, Hamelryck T. Langevin diffusions on the torus: estimation and applications Statistics and Computing. 29: 1-22. DOI: 10.1007/S11222-017-9790-2 |
0.305 |
|
| 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 |
0.46 |
|
| 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 |
0.647 |
|
| 2015 |
Bratholm LA, Christensen AS, Hamelryck T, Jensen JH. Bayesian inference of protein structure from chemical shift data. Peerj. 3: e861. PMID 25825683 DOI: 10.7717/Peerj.861 |
0.385 |
|
| 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 |
0.577 |
|
| 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 |
0.457 |
|
| 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 |
0.5 |
|
| 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 |
0.326 |
|
| 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 |
0.598 |
|
| 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, ... ... Hamelryck T, 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 |
0.619 |
|
| 2013 |
Johansson KE, Hamelryck T. A simple probabilistic model of multibody interactions in proteins. Proteins. 81: 1340-50. PMID 23468247 DOI: 10.1002/Prot.24277 |
0.47 |
|
| 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 |
0.386 |
|
| 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 |
0.598 |
|
| 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 |
0.368 |
|
| 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 |
0.628 |
|
| 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 |
0.478 |
|
| 2010 |
Stovgaard K, Andreetta C, Ferkinghoff-Borg J, Hamelryck T. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. Bmc Bioinformatics. 11: 429. PMID 20718956 DOI: 10.1186/1471-2105-11-429 |
0.365 |
|
| 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 |
0.418 |
|
| 2010 |
Paluszewski M, Hamelryck T. Mocapy++--a toolkit for inference and learning in dynamic Bayesian networks. Bmc Bioinformatics. 11: 126. PMID 20226024 DOI: 10.1186/1471-2105-11-126 |
0.365 |
|
| 2009 |
Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T. A probabilistic model of RNA conformational space. Plos Computational Biology. 5: e1000406. PMID 19543381 DOI: 10.1371/Journal.Pcbi.1000406 |
0.389 |
|
| 2009 |
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics (Oxford, England). 25: 1422-3. PMID 19304878 DOI: 10.1093/Bioinformatics/Btp163 |
0.322 |
|
| 2009 |
Hamelryck T. Probabilistic models and machine learning in structural bioinformatics. Statistical Methods in Medical Research. 18: 505-26. PMID 19153168 DOI: 10.1177/0962280208099492 |
0.411 |
|
| 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 |
0.513 |
|
| 2007 |
Won KJ, Hamelryck T, Prügel-Bennett A, Krogh A. An evolutionary method for learning HMM structure: prediction of protein secondary structure. Bmc Bioinformatics. 8: 357. PMID 17888163 DOI: 10.1186/1471-2105-8-357 |
0.418 |
|
| 2006 |
Paluszewski M, Hamelryck T, Winter P. Reconstructing protein structure from solvent exposure using tabu search. Algorithms For Molecular Biology : Amb. 1: 20. PMID 17069644 DOI: 10.1186/1748-7188-1-20 |
0.463 |
|
| 2006 |
Hamelryck T, Kent JT, Krogh A. Sampling realistic protein conformations using local structural bias. Plos Computational Biology. 2: e131. PMID 17002495 DOI: 10.1371/Journal.Pcbi.0020131 |
0.494 |
|
| 2006 |
Baranov PV, Vestergaard B, Hamelryck T, Gesteland RF, Nyborg J, Atkins JF. Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons. Biology Direct. 1: 28. PMID 16970810 DOI: 10.1186/1745-6150-1-28 |
0.531 |
|
| 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 |
0.416 |
|
| 2005 |
Hamelryck T. An amino acid has two sides: a new 2D measure provides a different view of solvent exposure. Proteins. 59: 38-48. PMID 15688434 DOI: 10.1002/Prot.20379 |
0.36 |
|
| 2003 |
Hamelryck T, Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics (Oxford, England). 19: 2308-10. PMID 14630660 DOI: 10.1093/Bioinformatics/Btg299 |
0.408 |
|
| 2003 |
Hamelryck T. Efficient identification of side-chain patterns using a multidimensional index tree. Proteins. 51: 96-108. PMID 12596267 DOI: 10.1002/Prot.10338 |
0.406 |
|
| 2001 |
Buts L, Dao-Thi MH, Loris R, Wyns L, Etzler M, Hamelryck T. Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus. Journal of Molecular Biology. 309: 193-201. PMID 11491289 DOI: 10.1006/Jmbi.2001.4639 |
0.648 |
|
| 2000 |
Hamelryck TW, Moore JG, Chrispeels MJ, Loris R, Wyns L. The role of weak protein-protein interactions in multivalent lectin-carbohydrate binding: crystal structure of cross-linked FRIL. Journal of Molecular Biology. 299: 875-83. PMID 10843844 DOI: 10.1006/Jmbi.2000.3785 |
0.524 |
|
| 1999 |
Bouckaert J, Hamelryck T, Wyns L, Loris R. Novel structures of plant lectins and their complexes with carbohydrates. Current Opinion in Structural Biology. 9: 572-7. PMID 10508764 DOI: 10.1016/S0959-440X(99)00007-X |
0.597 |
|
| 1999 |
Bouckaert J, Hamelryck TW, Wyns L, Loris R. The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A. The Journal of Biological Chemistry. 274: 29188-95. PMID 10506175 DOI: 10.1074/Jbc.274.41.29188 |
0.466 |
|
| 1999 |
Hamelryck TW, Loris R, Bouckaert J, Dao-Thi MH, Strecker G, Imberty A, Fernandez E, Wyns L, Etzler ME. Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus. Journal of Molecular Biology. 286: 1161-77. PMID 10047489 DOI: 10.1006/Jmbi.1998.2534 |
0.539 |
|
| 1998 |
Dao-Thi MH, Hamelryck TW, Bouckaert J, Körber F, Burkow V, Poortmans F, Etzler M, Strecker G, Wyns L, Loris R. Crystallization of two related lectins from the legume plant Dolichos biflorus. Acta Crystallographica. Section D, Biological Crystallography. 54: 1446-9. PMID 10089534 DOI: 10.1107/S0907444998004478 |
0.471 |
|
| 1998 |
Loris R, Hamelryck T, Bouckaert J, Wyns L. Legume lectin structure. Biochimica Et Biophysica Acta. 1383: 9-36. PMID 9546043 DOI: 10.1016/S0167-4838(97)00182-9 |
0.647 |
|
| 1996 |
Hamelryck TW, Poortmans F, Goossens A, Angenon G, Van Montagu M, Wyns L, Loris R. Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris. The Journal of Biological Chemistry. 271: 32796-802. PMID 8955116 DOI: 10.1074/Jbc.271.51.32796 |
0.595 |
|
| 1996 |
Hamelryck TW, Dao-Thi MH, Poortmans F, Chrispeels MJ, Wyns L, Loris R. The crystallographic structure of phytohemagglutinin-L. The Journal of Biological Chemistry. 271: 20479-85. PMID 8702788 DOI: 10.1074/Jbc.271.34.20479 |
0.555 |
|
| 1996 |
Dao-Thi MH, Hamelryck TW, Poortmans F, Voelker TA, Chrispeels MJ, Wyns L. Crystallization of glycosylated and nonglycosylated phytohemagglutinin-L. Proteins. 24: 134-7. PMID 8628728 DOI: 10.1002/(Sici)1097-0134(199601)24:1<134::Aid-Prot9>3.0.Co;2-K |
0.487 |
|
| 1995 |
Casset F, Hamelryck T, Loris R, Brisson JR, Tellier C, Dao-Thi MH, Wyns L, Poortmans F, Pérez S, Imberty A. NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction. The Journal of Biological Chemistry. 270: 25619-28. PMID 7592736 DOI: 10.1074/Jbc.270.43.25619 |
0.593 |
|
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