List of works - Thomas Hamelryck

A Generative Angular Model of Protein Structure Evolution ⬇️

scientific article

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

scientific article published on 22 April 2020

A generative, probabilistic model of local protein structure

scientific article

A probabilistic model of RNA conformational space ⬇️

scientific article

A simple probabilistic model of multibody interactions in proteins

scientific article

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

scientific article

An efficient null model for conformational fluctuations in proteins

scientific article published on 10 May 2012

An evolutionary method for learning HMM structure: prediction of protein secondary structure

scientific article

Bayesian inference of protein ensembles from SAXS data

scientific article

Bayesian inference of protein structure from chemical shift data.

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

article published in 1999

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

scientific article

Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris

scientific article

Crystallization of glycosylated and nonglycosylated phytohemagglutinin-L

scientific article published on 01 January 1996

Crystallization of glycosylated and nonglycosylated phytohemagglutinin‐L

scientific article published in January 1996

Crystallization of two related lectins from the legume plant Dolichos biflorus

scientific article published on November 1998

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

scientific article

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

scientific article published in April 2003

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

scientific article

Fast large-scale clustering of protein structures using Gauss integrals

scientific article published on 22 December 2011

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

scientific article

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.

scientific article

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

scientific article

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

scientific article published on 11 June 2020

Generative probabilistic models extend the scope of inferential structure determination

scientific article

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

scientific article

Legume lectin structure.

scientific article

Mixtures of concentrated multivariate sine distributions with applications to bioinformatics

scientific article published in November 2012

Mocapy++--a toolkit for inference and learning in dynamic Bayesian networks

scientific article

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

scientific article published on 29 May 2018

NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction

scientific article

Novel structures of plant lectins and their complexes with carbohydrates.

scientific article

PDB file parser and structure class implemented in Python

scientific article published in November 2003

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

scientific article

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

scientific article

Probabilistic Determination of Native State Ensembles of Proteins

scientific article published on 30 June 2014

Probabilistic Models of Local Biomolecular Structure and Their Applications

Probabilistic models and machine learning in structural bioinformatics.

scientific article

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

scientific article (publication date: 2013)

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

Reconstructing protein structure from solvent exposure using tabu search.

scientific article

Sampling realistic protein conformations using local structural bias ⬇️

scientific article

Subtle Monte Carlo Updates in Dense Molecular Systems

scientific article published on 18 January 2012

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

scientific article

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

article

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

scientific article

List of works by Thomas Hamelryck

A Generative Angular Model of Protein Structure Evolution ⬇️

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

A generative, probabilistic model of local protein structure

A probabilistic model of RNA conformational space ⬇️

A simple probabilistic model of multibody interactions in proteins

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

An efficient null model for conformational fluctuations in proteins

An evolutionary method for learning HMM structure: prediction of protein secondary structure

Bayesian inference of protein ensembles from SAXS data

Bayesian inference of protein structure from chemical shift data.

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

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

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

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

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

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

Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris

Crystallization of glycosylated and nonglycosylated phytohemagglutinin-L

Crystallization of glycosylated and nonglycosylated phytohemagglutinin‐L

Crystallization of two related lectins from the legume plant Dolichos biflorus

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

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

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

Fast large-scale clustering of protein structures using Gauss integrals

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

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.

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

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

Generative probabilistic models extend the scope of inferential structure determination

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

Legume lectin structure.

Mixtures of concentrated multivariate sine distributions with applications to bioinformatics

Mocapy++--a toolkit for inference and learning in dynamic Bayesian networks

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction

Novel structures of plant lectins and their complexes with carbohydrates.

PDB file parser and structure class implemented in Python

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

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

Probabilistic Determination of Native State Ensembles of Proteins

Probabilistic Models of Local Biomolecular Structure and Their Applications

Probabilistic models and machine learning in structural bioinformatics.

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

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

Reconstructing protein structure from solvent exposure using tabu search.

Sampling realistic protein conformations using local structural bias ⬇️

Subtle Monte Carlo Updates in Dense Molecular Systems

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

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

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