Zobrazeno 1 - 10
of 212
pro vyhledávání: '"Jan H Jensen"'
Publikováno v:
Beilstein Journal of Organic Chemistry, Vol 20, Iss 1, Pp 1614-1622 (2024)
Determining the pKa values of various C–H sites in organic molecules offers valuable insights for synthetic chemists in predicting reaction sites. As molecular complexity increases, this task becomes more challenging. This paper introduces pKalcula
Externí odkaz:
https://doaj.org/article/53af7e7564aa4185b0bd4a69daa3f9e8
Publikováno v:
PLoS ONE, Vol 9, Iss 2, p e88800 (2014)
The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where th
Externí odkaz:
https://doaj.org/article/e009789a3172446cb1586dfb097f6503
Publikováno v:
PLoS ONE, Vol 9, Iss 5, p e95833 (2014)
HIV-1 protease represents an appealing system for directed enzyme re-design, since it has various different endogenous targets, a relatively simple structure and it is well studied. Recently Chaudhury and Gray (Structure (2009) 17: 1636-1648) publish
Externí odkaz:
https://doaj.org/article/e5e72c6fe5074f11a685360c2d3d5bb1
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 4, p e60602 (2013)
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach effi
Externí odkaz:
https://doaj.org/article/6418afa54bc849cb904c517047e88242
Publikováno v:
PLoS ONE, Vol 8, Iss 7, p e67725 (2013)
An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is
Externí odkaz:
https://doaj.org/article/79b63ad41ed941eb874bbcdfe87f7bf2
Publikováno v:
Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-17 (2023)
Abstract With the increasingly more important role of machine learning (ML) models in chemical research, the need for putting a level of confidence to the model predictions naturally arises. Several methods for obtaining uncertainty estimates have be
Externí odkaz:
https://doaj.org/article/ed0651e907dd46c78f2bfbd9571ea303
Publikováno v:
PLoS ONE, Vol 7, Iss 12, p e49849 (2012)
We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors. The methodo
Externí odkaz:
https://doaj.org/article/40704339941b41f99d0c1933e5fc335c
Publikováno v:
PLoS ONE, Vol 7, Iss 7, p e41117 (2012)
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins.
Externí odkaz:
https://doaj.org/article/6b15af8c1652470f9578d0aeab049eda
Publikováno v:
PLoS ONE, Vol 7, Iss 9, p e44480 (2012)
Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without ex
Externí odkaz:
https://doaj.org/article/d186f1ea1c454b95af4867d30b51c770