Zobrazeno 1 - 10
of 82
pro vyhledávání: '"Thomas Hamelryck"'
Publikováno v:
PeerJ, Vol 8, p e9159 (2020)
The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots,
Externí odkaz:
https://doaj.org/article/69f167dedf76467ea34ce073b6dc248e
Autor:
Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan Schneider
Publikováno v:
F1000Research, Vol 9 (2020)
Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics communi
Externí odkaz:
https://doaj.org/article/1660ea70c64c4317965e8da16a60148b
Publikováno v:
PeerJ, Vol 3, p e861 (2015)
Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor
Externí odkaz:
https://doaj.org/article/9b62e5078a5e42ef9a5ce373e48c0172
Publikováno v:
PeerJ, Vol 2, p e277 (2014)
We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually speci
Externí odkaz:
https://doaj.org/article/c31bbd0e7a374c98b4ba2630c32fd2f9
Autor:
Anders S Christensen, Troels E Linnet, Mikael Borg, Wouter Boomsma, Kresten Lindorff-Larsen, Thomas Hamelryck, Jan H Jensen
Publikováno v:
PLoS ONE, Vol 8, Iss 12, p e84123 (2013)
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 hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechan
Externí odkaz:
https://doaj.org/article/9f079b2f1048401fa17f7f41ae4de6e7
Publikováno v:
PLoS ONE, Vol 8, Iss 11, p e79439 (2013)
We present the theoretical foundations of a general principle to infer structure ensembles of flexible biomolecules from spatially and temporally averaged data obtained in biophysical experiments. The central idea is to compute the Kullback-Leibler o
Externí odkaz:
https://doaj.org/article/82e5221da54d4a39b8ff25a9eff393d0
Autor:
Thomas Hamelryck, Mikael Borg, Martin Paluszewski, Jonas Paulsen, Jes Frellsen, Christian Andreetta, Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg
Publikováno v:
PLoS ONE, Vol 5, Iss 11, p e13714 (2010)
Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge-based potentials based on pairwise distances--so-called "potentials of mean force" (PMFs)--have been center stage in the
Externí odkaz:
https://doaj.org/article/45f90bfcdbad41b88281a3c31ce063c1
Autor:
Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck
Publikováno v:
PLoS Computational Biology, Vol 5, Iss 6, p e1000406 (2009)
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 case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accura
Externí odkaz:
https://doaj.org/article/40f5cd202b474cacb055f9a358bb7385
Publikováno v:
PLoS Computational Biology, Vol 2, Iss 9, p e131 (2006)
The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method
Externí odkaz:
https://doaj.org/article/7791692145fd4d04ad6a4ba824cf7700
Publikováno v:
AI & SOCIETY.
Deep learning developers typically rely on deep learning software frameworks (DLSFs)—simply described as pre-packaged libraries of programming components that provide high-level access to deep learning functionality. New DLSFs progressively encapsu
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::90baf9126727c48e9154646a2ca9372e
https://doi.org/10.1007/s00146-023-01688-z
https://doi.org/10.1007/s00146-023-01688-z