T. Hamelryck

发表

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

J. F. Atkins, R. Gesteland, P. Baranov, 2006, Biology Direct.

Inference of Structure Ensembles of Flexible Biomolecules from Sparse, Averaged Data

K. Mardia, J. Frellsen, T. Hamelryck, 2013, PloS one.

A generative, probabilistic model of local protein structure

Jesper Ferkinghoff-Borg, Thomas Hamelryck, Kanti V Mardia, 2008, Proceedings of the National Academy of Sciences.

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

K. Mardia, Sandro Bottaro, J. Frellsen, 2014, Proteins.

Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem

Jesper Illemann Foldager, D. Theobald, J. Frellsen, 2015 .

Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized

Sandro Bottaro, J. Frellsen, T. Hamelryck, 2010, PloS one.

Towards a General Probabilistic Model of Protein Structure: The Reference Ratio Method

Kanti V. Mardia, Jes Frellsen, Jesper Ferkinghoff-Borg, 2012 .

NMR, Molecular Modeling, and Crystallographic Studies of Lentil Lectin-Sucrose Interaction (*)

J. Brisson, L. Wyns, A. Imberty, 1995, Journal of Biological Chemistry.

Hyeongki Kim Dihedral angle prediction using generative adversarial networks

T. Hamelryck, Hyeongki Kim, 2018 .

An amino acid has two sides: A new 2D measure provides a different view of solvent exposure

T. Hamelryck, 2005, Proteins.

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

Kresten Lindorff-Larsen, Michele Vendruscolo, Wouter Boomsma, 2014, Proceedings of the National Academy of Sciences.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

Kresten Lindorff-Larsen, Jan H. Jensen, Wouter Boomsma, 2013, PloS one.

A Generative Angular Model of Protein Structure Evolution

K. Mardia, M. Sørensen, J. Hein, 2016, Molecular biology and evolution.

Using the Fisher-Bingham distribution in stochastic models for protein structure

Thomas Hamelryck, John T. Kent, J. Kent, 2022 .

Mixtures of concentrated multivariate sine distributions with applications to bioinformatics

Kanti V. Mardia, Charles C. Taylor, Thomas Hamelryck, 2012 .

An efficient null model for conformational fluctuations in proteins.

Sandro Bottaro, T. Hamelryck, J. Ferkinghoff-Borg, 2012, Structure.

Crystal Structure of Arcelin-5, a Lectin-like Defense Protein from Phaseolus vulgaris*

M. Van Montagu, L. Wyns, T. Hamelryck, 1996, The Journal of Biological Chemistry.

Experimental Results: Comparison of CN and HSE

P. Winter, T. Hamelryck, M. Paluszewski, 2005 .

Crystallization of glycosylated and nonglycosylated phytohemagglutinin‐L

L. Wyns, T. Hamelryck, T. Voelker, 1996, Proteins.

CRYSTALLIZATION ANNOUNCEMENTS Crystallization of Glycosylated and Nonglycosylated Phytohemagglutinin-L

T. Hamelryck, T. Voelker, M. Dao-Thi, 1996 .

Accelerating vaccine development through a deep probabilistic programming approach to protein structure prediction

Ahmad Salim Al-Sibahi, Christian B. Thygesen, T. Hamelryck, 2022 .

Langevin diffusions on the torus: estimation and applications

K. Mardia, M. Sørensen, T. Hamelryck, 2017, Statistics and Computing.

Langevin diffusions on the torus: estimation and applications

Kanti V. Mardia, Thomas Hamelryck, Michael Sørensen, 2017, Statistics and Computing.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Bartek Wilczynski, Thomas Hamelryck, Jeffrey T. Chang, 2009, Bioinform..

Probabilistic Determination of Native State Ensembles of Proteins.

Kresten Lindorff-Larsen, Wouter Boomsma, Jesper Ferkinghoff-Borg, 2014, Journal of chemical theory and computation.

Novel structures of plant lectins and their complexes with carbohydrates.

L. Wyns, T. Hamelryck, R. Loris, 1999, Current opinion in structural biology.

The role of weak protein-protein interactions in multivalent lectin-carbohydrate binding: crystal structure of cross-linked FRIL.

L. Wyns, T. Hamelryck, R. Loris, 2000, Journal of molecular biology.

The Crystal Structures of Man(α1–3)Man(α1-O)Me and Man(α1–6)Man(α1-O)Me in Complex with Concanavalin A*

L. Wyns, T. Hamelryck, R. Loris, 1999, The Journal of Biological Chemistry.

Legume lectin structure.

L. Wyns, T. Hamelryck, R. Loris, 1998, Biochimica et biophysica acta.

Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model

Thomas Hamelryck, Ahmad Salim Al-Sibahi, Christian B. Thygesen, 2021, bioRxiv.

Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus.

L. Wyns, T. Hamelryck, M. Etzler, 2001, Journal of molecular biology.

Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.

L. Wyns, A. Imberty, T. Hamelryck, 1999, Journal of molecular biology.

PDB file parser and structure class implemented in Python

Bernard Manderick, Thomas Hamelryck, B. Manderick, 2003, Bioinform..

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

Toroidal Diffusions and Protein Structure Evolution

Kanti V. Mardia, Michael Sørensen, Thomas Hamelryck, 2018, Applied Directional Statistics.

Probabilistic models and machine learning in structural bioinformatics

Thomas Hamelryck, T. Hamelryck, 2009, Statistical methods in medical research.

Efficient identification of side‐chain patterns using a multidimensional index tree

Thomas Hamelryck, T. Hamelryck, 2003, Proteins.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck, 2016, Journal of molecular biology.

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

Wouter Boomsma, Jes Frellsen, Tim Harder, 2010, BMC Bioinformatics.

On the significance of the reference ratio method in inferential structure determination of biomolecules

T. Hamelryck, S. Olsson, 2013 .

Sampling Realistic Protein Conformations Using Local Structural Bias

Anders Krogh, Thomas Hamelryck, John T. Kent, 2006, PLoS Comput. Biol..

Subtle Monte Carlo Updates in Dense Molecular Systems.

Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg, 2012, Journal of chemical theory and computation.

Full cyclic coordinate descent: solving the protein loop closure problem in Cα space

Wouter Boomsma, Thomas Hamelryck, T. Hamelryck, 2005, BMC Bioinformatics.

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

Kresten Lindorff-Larsen, Pengfei Tian, Jan H. Jensen, 2013, J. Comput. Chem..

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

Jesper Ferkinghoff-Borg, Thomas Hamelryck, Christian Andreetta, 2010, BMC Bioinformatics.

Mixture models for spherical data with applications to protein bioinformatics

K. Mardia, J. Kent, T. Hamelryck, 2021, 2104.13140.

Generative probabilistic models extend the scope of inferential structure determination.

Simon Olsson, Wouter Boomsma, Jes Frellsen, 2011, Journal of magnetic resonance.

A Probabilistic Model of RNA Conformational Space

Kanti V. Mardia, Jes Frellsen, Jesper Ferkinghoff-Borg, 2009, PLoS Comput. Biol..

Crystallization of two related lectins from the legume plant Dolichos biflorus.

L. Wyns, T. Hamelryck, M. Etzler, 1998, Acta crystallographica. Section D, Biological crystallography.

The Crystallographic Structure of Phytohemagglutinin-L*

L. Wyns, T. Hamelryck, R. Loris, 1996, The Journal of Biological Chemistry.

Bayesian inference of protein ensembles from SAXS data.

L. D. Antonov, S. Olsson, W. Boomsma, 2016, Physical chemistry chemical physics : PCCP.

Structural Features of the Legume Lectins

Lode Wyns, Thomas Hamelryck, Remy Loris, 1998 .

Bayesian inference of protein structure from chemical shift data

Jan H. Jensen, Thomas Hamelryck, Lars A. Bratholm, 2015, PeerJ.

A Probabilistic Programming Approach to Protein Structure Superposition

Thomas Hamelryck, Lys Sanz Moreta, Ahmad Salim Al-Sibahi, 2019, bioRxiv.

Bayesian Methods in Structural Bioinformatics

Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck, 2012 .

Persistent topology of protein space

J. Marron, T. Hamelryck, J. Borgert, 2021, 2102.06768.

Evolving hidden Markov models for protein secondary structure prediction

Adam Prügel-Bennett, Anders Krogh, Thomas Hamelryck, 2005, 2005 IEEE Congress on Evolutionary Computation.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

K. E. Johansson, K. Lindorff-Larsen, T. Hamelryck, 2016, Journal of molecular biology.

Bayesian inference of protein ensembles from SAXS data.

L. D. Antonov, T. Hamelryck, S. Olsson, 2016, Physical chemistry chemical physics : PCCP.

Bayesian protein superposition using Hamiltonian Monte Carlo

Thomas Hamelryck, Lys Sanz Moreta, Ahmad Salim Al-Sibahi, 2020, 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE).

GISA: using Gauss Integrals to identify rare conformations in protein structures

Thomas Hamelryck, Peter Røgen, Christian Grønbæk, 2019, bioRxiv.

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

K. E. Johansson, J. Frellsen, T. Hamelryck, 2010, BMC Bioinformatics.

Fast large-scale clustering of protein structures using Gauss integrals

Wouter Boomsma, Tim Harder, Thomas Hamelryck, 2012, Bioinform..

Bayesian inference of protein ensembles from SAXS data

L. D. Antonov, T. Hamelryck, S. Olsson, 2016 .