Zobrazeno 1 - 10
of 482
pro vyhledávání: '"Wilfred F. van Gunsteren"'
Publikováno v:
European Biophysics Journal, 51 (3)
In protein simulation or structure refinement based on values of observable quantities measured in (aqueous) solution, solvent (water) molecules may be explicitly treated, omitted, or represented by a potential of mean-solvation-force term, depending
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b89f23684383ce175b04474d79454fd1
https://doi.org/10.1007/s00249-022-01593-1
https://doi.org/10.1007/s00249-022-01593-1
Publikováno v:
Proteins: Structure, Function and Bioinformatics, 90 (2)
Computer simulation of proteins in aqueous solution at the atomic level of resolution is still limited in time span and system size due to limited computing power available and thus employs a variety of time-saving techniques that trade some accuracy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::61f51dfae9af705da8e94dcb60f629c8
https://doi.org/10.1002/prot.26251
https://doi.org/10.1002/prot.26251
A method for structure refinement of molecules based on residual dipolar coupling (RDC) data is proposed. It calculates RDC values using rotational and molecule-internal configurational sampling instead of the common refinement procedure that is base
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fd1855ed1000678954967be5067904ae
https://ora.ox.ac.uk/objects/uuid:ffe159a8-126b-4d97-af13-723e7261ed67
https://ora.ox.ac.uk/objects/uuid:ffe159a8-126b-4d97-af13-723e7261ed67
Autor:
Michael M H Graf, Lin Zhixiong, Urban Bren, Dietmar Haltrich, Wilfred F van Gunsteren, Chris Oostenbrink
Publikováno v:
PLoS Computational Biology, Vol 10, Iss 12, p e1003995 (2014)
The flavoenzyme pyranose dehydrogenase (PDH) from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation. This promiscuous substrate specificity makes PDH a promising catalyst for bi
Externí odkaz:
https://doaj.org/article/c7682c21f6d841789ed682e3520310c4
Publikováno v:
Journal of Chemical Information and Modeling. 59:2218-2230
Epothilones are among the most potent chemotherapeutic drugs used for the treatment of cancer. Epothilone A (EpoA), a natural product, is a macrocyclic molecule containing 34 non-hydrogen atoms and a thiazole side chain. NMR studies of EpoA in aqueou
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8fe1a9c9c664191f3fbee58fa2556491
https://doi.org/10.1021/acs.jcim.9b00171
https://doi.org/10.1021/acs.jcim.9b00171
Autor:
Manuel M Müller, Jane R Allison, Narupat Hongdilokkul, Laurent Gaillon, Peter Kast, Wilfred F van Gunsteren, Philippe Marlière, Donald Hilvert
Publikováno v:
PLoS Genetics, Vol 9, Iss 1, p e1003187 (2013)
The contemporary proteinogenic repertoire contains 20 amino acids with diverse functional groups and side chain geometries. Primordial proteins, in contrast, were presumably constructed from a subset of these building blocks. Subsequent expansion of
Externí odkaz:
https://doaj.org/article/0f687fdbf2764a9ca772733f50d682da
Autor:
Alan E. Mark, Xavier Daura, Wilfred F. van Gunsteren, Sereina Riniker, Chris Oostenbrink, Philippe H. Hünenberger, Bruno A. C. Horta, Niels Hansen, Maria Pechlaner, Patrick F.J. Fuchs
Publikováno v:
Chemphyschem : a European journal of chemical physics and physical chemistry. 22(3)
Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, bi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f53a5a49327bd1512c694c530c4d973
https://pubmed.ncbi.nlm.nih.gov/33377305
https://pubmed.ncbi.nlm.nih.gov/33377305
Publikováno v:
ChemBioChem, 22 (6)
Chembiochem
Chembiochem
Values of S2CH and S2NH order parameters derived from NMR relaxation measurements on proteins cannot be used straightforwardly to determine protein structure because they cannot be related to a single protein structure, but are defined in terms of an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::806aa3f1bfa5fa05c8c6c2d0a24f7d57
https://doi.org/10.1002/cbic.202000674
https://doi.org/10.1002/cbic.202000674
Publikováno v:
Journal of computational chemistryREFERENCES. 42(6)
An algorithm to apply bond-angle constraints in molecular dynamics simulations of macromolecules or molecular liquids is presented. It uses Cartesian coordinates and determines the Lagrange multipliers required for maintaining the constraints iterati
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f96f8fef25dfc17706fab880cb4fa89e
https://pubmed.ncbi.nlm.nih.gov/33351979
https://pubmed.ncbi.nlm.nih.gov/33351979
Publikováno v:
The Journal of chemical physics. 152(2)
Various algorithms to apply dihedral-angle constraints in molecular dynamics or stochastic dynamics simulations of molecular systems are presented, investigated, and tested. They use Cartesian coordinates and determine the Lagrangian multipliers nece
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fd108d740e5ce9dc17d0c61b07a8f62e
https://pubmed.ncbi.nlm.nih.gov/31941329
https://pubmed.ncbi.nlm.nih.gov/31941329