Search Results - "Hamelryck, Thomas"

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

“…The concept of amino acid solvent exposure is crucial for understanding and predicting various aspects of protein structure and function. The traditional…”
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Biopython: freely available Python tools for computational molecular biology and bioinformatics by Cock, Peter J. A., Antao, Tiago, Chang, Jeffrey T., Chapman, Brad A., Cox, Cymon J., Dalke, Andrew, Friedberg, Iddo, Hamelryck, Thomas, Kauff, Frank, Wilczynski, Bartek, de Hoon, Michiel J. L.

“…The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of…”
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Inference of structure ensembles of flexible biomolecules from sparse, averaged data by Olsson, Simon, Frellsen, Jes, Boomsma, Wouter, Mardia, Kanti V, Hamelryck, Thomas

“…We present the theoretical foundations of a general principle to infer structure ensembles of flexible biomolecules from spatially and temporally averaged data…”
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GISA: using Gauss Integrals to identify rare conformations in protein structures by Grønbæk, Christian, Hamelryck, Thomas, Røgen, Peter

“…The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However,…”
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Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models by Stovgaard, Kasper, Andreetta, Christian, Ferkinghoff-Borg, Jesper, Hamelryck, Thomas

“…Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution…”
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PDB file parser and structure class implemented in Python by Hamelryck, Thomas, Manderick, Bernard

“…The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with…”
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Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts by Boomsma, Wouter, Tian, Pengfei, Frellsen, Jes, Ferkinghoff-Borg, Jesper, Hamelryck, Thomas, Lindorff-Larsen, Kresten, Vendruscolo, Michele

“…Significance Chemical shifts are the most fundamental parameters measured in nuclear magnetic resonance spectroscopy. Since these parameters are exquisitely…”
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Probabilistic Determination of Native State Ensembles of Proteins by Olsson, Simon, Vögeli, Beat Rolf, Cavalli, Andrea, Boomsma, Wouter, Ferkinghoff-Borg, Jesper, Lindorff-Larsen, Kresten, Hamelryck, Thomas

“…The motions of biological macromolecules are tightly coupled to their functions. However, while the study of fast motions has become increasingly feasible in…”
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generative, probabilistic model of local protein structure by Boomsma, Wouter, Mardia, Kanti V, Taylor, Charles C, Ferkinghoff-Borg, Jesper, Krogh, Anders, Hamelryck, Thomas

“…Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology…”
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Sampling realistic protein conformations using local structural bias by Hamelryck, Thomas, Kent, John T, Krogh, Anders

“…The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make…”
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Mocapy++--a toolkit for inference and learning in dynamic Bayesian networks by Paluszewski, Martin, Hamelryck, Thomas

“…Mocapy++ is a toolkit for parameter learning and inference in dynamic Bayesian networks (DBNs). It supports a wide range of DBN architectures and probability…”
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Fast large-scale clustering of protein structures using Gauss integrals by Harder, Tim, Borg, Mikael, Boomsma, Wouter, Røgen, Peter, Hamelryck, Thomas

“…Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a…”
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Potentials of mean force for protein structure prediction vindicated, formalized and generalized by Hamelryck, Thomas, Borg, Mikael, Paluszewski, Martin, Paulsen, Jonas, Frellsen, Jes, Andreetta, Christian, Boomsma, Wouter, Bottaro, Sandro, Ferkinghoff-Borg, Jesper

“…Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge-based potentials based on…”
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A probabilistic model of RNA conformational space by Frellsen, Jes, Moltke, Ida, Thiim, Martin, Mardia, Kanti V, Ferkinghoff-Borg, Jesper, Hamelryck, Thomas

“…The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the…”
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Beyond rotamers: a generative, probabilistic model of side chains in proteins by Harder, Tim, Boomsma, Wouter, Paluszewski, Martin, Frellsen, Jes, Johansson, Kristoffer E, Hamelryck, Thomas

“…Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high…”
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Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics by Christensen, Anders S, Linnet, Troels E, Borg, Mikael, Boomsma, Wouter, Lindorff-Larsen, Kresten, Hamelryck, Thomas, Jensen, Jan H

“…We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key…”
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PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure by Boomsma, Wouter, Frellsen, Jes, Harder, Tim, Bottaro, Sandro, Johansson, Kristoffer E., Tian, Pengfei, Stovgaard, Kasper, Andreetta, Christian, Olsson, Simon, Valentin, Jan B., Antonov, Lubomir D., Christensen, Anders S., Borg, Mikael, Jensen, Jan H., Lindorff-Larsen, Kresten, Ferkinghoff-Borg, Jesper, Hamelryck, Thomas

“…We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package…”
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An evolutionary method for learning HMM structure: prediction of protein secondary structure by Won, Kyoung-Jae, Hamelryck, Thomas, Prügel-Bennett, Adam, Krogh, Anders

“…The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of…”
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A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) by Orengo, Christine, Velankar, Sameer, Wodak, Shoshana, Zoete, Vincent, Bonvin, Alexandre M.J.J., Elofsson, Arne, Feenstra, K. Anton, Gerloff, Dietland L., Hamelryck, Thomas, Hancock, John M., Helmer-Citterich, Manuela, Hospital, Adam, Orozco, Modesto, Perrakis, Anastassis, Rarey, Matthias, Soares, Claudio, Sussman, Joel L., Thornton, Janet M., Tuffery, Pierre, Tusnady, Gabor, Wierenga, Rikkert, Salminen, Tiina, Schneider, Bohdan

“…Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the…”
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Generative probabilistic models extend the scope of inferential structure determination by Olsson, Simon, Boomsma, Wouter, Frellsen, Jes, Bottaro, Sandro, Harder, Tim, Ferkinghoff-Borg, Jesper, Hamelryck, Thomas

“…[Display omitted] ► Generative probabilistic models in inferential structure determination are examined. ► We observe increased efficiency and precision…”
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