Thomas Hamelryck

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Remy LorisHoogleraar, VUBVerified email at vub.be
Wouter BoomsmaProfessor, Department of Computer Science, University of CopenhagenVerified email at di.ku.dk
Jesper Ferkinghoff-BorgAssociate Professor, Research Director, Novo Nordisk A/SVerified email at novonordisk.com
Kanti MardiaSENIOR RESARCH PROFESSOR ,UNIVERSITY OF LEEDS AND UNIVERSITY OF OXFORDVerified email at leeds.ac.uk
Jes FrellsenAssociate Professor, Technical University of Denmark (DTU)Verified email at dtu.dk
Julie BouckaertUnite de Glycobiologie Structurale et FonctionelleVerified email at univ-lille.fr
Iddo FriedbergAssociate Professor of Bioinformatics, Iowa State UniversityVerified email at iastate.edu
Tiago AntaoUniversity of MontanaVerified email at cam.ac.uk
Peter CockJames Hutton Institute (formerly known as the Scottish Crop Research Institute)Verified email at hutton.ac.uk
Christian AndreettaUniv. of Copenhagen, Denmark, and Uni Computing, Uni Research, NorwayVerified email at uni.no
Simon OlssonAssistant Professor, Chalmers University of TechnologyVerified email at chalmers.se
Sandro BottaroPeptoneVerified email at peptone.io
Tim HarderResearch Scientist at Philips ResearchVerified email at philips.com
Anders KroghDepartment of Computer Science and Center for Health Data Science, University of CopenhagenVerified email at di.ku.dk
Kristoffer Enøe JohanssonDepartment of Biology, University of CopenhagenVerified email at bio.ku.dk
Charles C TaylorUniversity of LeedsVerified email at maths.leeds.ac.uk
Kresten Lindorff-LarsenLinderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenVerified email at bio.ku.dk
Kasper StovgaardBioinformatics Centre, University of CopenhagenVerified email at ihfood.dk
Lubomir D. AntonovPhD Fellow, University of CopenhagenVerified email at binf.ku.dk
Jan H. JensenUniversity of CopenhagenVerified email at chem.ku.dk

Thomas Hamelryck

Dpt. of computer science / Dpt. of biology, University of Copenhagen

Verified email at binf.ku.dk - Homepage

Deep probabilistic programming Bayesian statistics Bioinformatics


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Biopython: freely available Python tools for computational molecular biology and bioinformatics PJA Cock, T Antao, JT Chang, BA Chapman, CJ Cox, A Dalke, I Friedberg, ... Bioinformatics 25 (11), 1422, 2009	4496	2009
Legume lectin structure R Loris, T Hamelryck, J Bouckaert, L Wyns Biochimica et biophysica acta (BBA)-Protein structure and molecular …, 1998	755	1998
PDB file parser and structure class implemented in Python T Hamelryck, B Manderick Bioinformatics 19 (17), 2308-2310, 2003	271	2003
A generative, probabilistic model of local protein structure W Boomsma, KV Mardia, CC Taylor, J Ferkinghoff-Borg, A Krogh, ... Proceedings of the National Academy of Sciences 105 (26), 8932-8937, 2008	194	2008
An amino acid has two sides: a new 2D measure provides a different view of solvent exposure T Hamelryck Proteins: Structure, Function, and Bioinformatics 59 (1), 38-48, 2005	175	2005
Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers fromDolichos biflorus TW Hamelryck, R Loris, J Bouckaert, MH Dao-Thi, G Strecker, A Imberty, ... Journal of molecular biology 286 (4), 1161-1177, 1999	165	1999
The crystallographic structure of phytohemagglutinin-L TW Hamelryck, MH Dao-Thi, F Poortmans, MJ Chrispeels, L Wyns, ... Journal of Biological Chemistry 271 (34), 20479-20485, 1996	160	1996
Sampling realistic protein conformations using local structural bias T Hamelryck, JT Kent, A Krogh PLoS Computational Biology 2 (9), e131, 2006	147	2006
A probabilistic model of RNA conformational space J Frellsen, I Moltke, M Thiim, KV Mardia, J Ferkinghoff-Borg, T Hamelryck PLoS computational biology 5 (6), e1000406, 2009	120	2009
Novel structures of plant lectins and their complexes with carbohydrates J Bouckaert, T Hamelryck, L Wyns, R Loris Current opinion in structural biology 9 (5), 572-577, 1999	111	1999
Potentials of mean force for protein structure prediction vindicated, formalized and generalized T Hamelryck, M Borg, M Paluszewski, J Paulsen, J Frellsen, C Andreetta, ... PloS one 5 (11), e13714, 2010	97	2010
Beyond rotamers: a generative, probabilistic model of side chains in proteins T Harder, W Boomsma, M Paluszewski, J Frellsen, KE Johansson, ... BMC bioinformatics 11, 1-13, 2010	80	2010
NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction F Casset, T Hamelryck, R Loris, JR Brisson, C Tellier, MH Dao-Thi, ... Journal of Biological Chemistry 270 (43), 25619-25628, 1995	80	1995
An evolutionary method for learning HMM structure: prediction of protein secondary structure KJ Won, T Hamelryck, A Prügel-Bennett, A Krogh BMC bioinformatics 8 (1), 1-13, 2007	68	2007
The crystal structures of Man (α1–3) Man (α1-O) Me and Man (α1–6) Man (α1-O) Me in complex with concanavalin A J Bouckaert, TW Hamelryck, L Wyns, R Loris Journal of Biological Chemistry 274 (41), 29188-29195, 1999	68	1999
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models K Stovgaard, C Andreetta, J Ferkinghoff-Borg, T Hamelryck BMC bioinformatics 11 (1), 1-14, 2010	65	2010
Inference of structure ensembles of flexible biomolecules from sparse, averaged data S Olsson, J Frellsen, W Boomsma, KV Mardia, T Hamelryck PloS one 8 (11), e79439, 2013	58	2013
Bayesian inference of protein ensembles from SAXS data LD Antonov, S Olsson, W Boomsma, T Hamelryck Physical Chemistry Chemical Physics 18 (8), 5832-5838, 2016	56	2016
Bayesian methods in structural bioinformatics T Hamelryck, K Mardia, J Ferkinghoff-Borg Springer, 2012	54	2012
The role of weak protein-protein interactions in multivalent lectin-carbohydrate binding: crystal structure of cross-linked FRIL TW Hamelryck, JG Moore, MJ Chrispeels, R Loris, L Wyns Journal of Molecular Biology 299 (4), 875-883, 2000	52	2000

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