Zobrazeno 1 - 10
of 156
pro vyhledávání: '"Philippe H. Hünenberger"'
Publikováno v:
Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-22 (2023)
Abstract This article documents enu, a freely-downloadable, open-source and stand-alone program written in C++ for the enumeration of the constitutional isomers and stereoisomers of a molecular formula. The program relies on graph theory to enumerate
Externí odkaz:
https://doaj.org/article/8bc94fdc8bd14aa49e597df6d1760fbe
Autor:
Salomé R. Rieder, Benjamin Ries, Candide Champion, Emilia P. Barros, Philippe H. Hünenberger, Sereina Riniker
Publikováno v:
CHIMIA, Vol 76, Iss 4 (2022)
Molecular dynamics (MD) simulations have become an important tool to investigate biological systems. Free-energy calculations based on MD are playing an increasingly important role for computer-aided drug design and material discovery in recent years
Externí odkaz:
https://doaj.org/article/b2ee70b969c4401e80b4f5426cae21c3
Publikováno v:
CHIMIA, Vol 55, Iss 10 (2001)
Electrostatic interactions are of fundamental importance in determining the structure, dynamics, and function of biomolecules. In particular, they play a key role in protein folding and stability, pH-induced conformational changes, recognition of sub
Externí odkaz:
https://doaj.org/article/f5837156349c40329ac68058375b0ff4
Autor:
Marina P. Oliveira, Yan M. H. Gonçalves, S. Kashef Ol Gheta, Salomé R. Rieder, Bruno A. C. Horta, Philippe H. Hünenberger
Publikováno v:
Journal of Chemical Theory and Computation, 18 (11)
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), includ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c081739e37a246aa7eb74f3247b56fab
https://doi.org/10.1021/acs.jctc.2c00524
https://doi.org/10.1021/acs.jctc.2c00524
Autor:
Yan M. H. Gonçalves, Sadra Kashefolgheta, Marina P. Oliveira, Philippe H. Hünenberger, Bruno A. C. Horta
Publikováno v:
Journal of Computational Chemistry, 43 (9)
The calibration of torsional interaction terms by fitting relative gas-phase conformational energies against their quantum-mechanical values is a common procedure in force-field development. However, much less attention has been paid to the optimizat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::783c6379ee9ce640fdf332a37e97e5d5
https://doi.org/10.1002/jcc.26819
https://doi.org/10.1002/jcc.26819
Publikováno v:
Journal of Chemical Theory and Computation, 17 (9)
Alchemical free energy calculations generally require intermediate states along a coupling parameter lambda to establish sufficient phase space overlap for obtaining converged results. Such intermediate states can also be engineered to lower the ener
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e64b429b5c83d9cc8a7800aa08e3f117
https://doi.org/10.1021/acs.jctc.1c00418
https://doi.org/10.1021/acs.jctc.1c00418
Autor:
Salomé R. Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emilia P. Barros, Philippe H. Hünenberger, Sereina Riniker
Publikováno v:
Journal of Chemical Information and Modeling, 62 (12)
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's acceptance ratio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4c81f897a089cecd156994cc0a8b1d8
https://hdl.handle.net/20.500.11850/557014
https://hdl.handle.net/20.500.11850/557014
Publikováno v:
The Journal of Physical Chemistry B, 126 (25)
Molecular dynamics studies have demonstrated that molecular water at an interface, with either a gas or a solid, displays anisotropic orientational behavior in contrast to its bulk counterpart. This effect has been recently implicated in the like-cha
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d45ea6b115c8cc2fc439b9a73e0f324b
https://pubmed.ncbi.nlm.nih.gov/35726865
https://pubmed.ncbi.nlm.nih.gov/35726865
Publikováno v:
Physical Chemistry Chemical Physics
Physical Chemistry Chemical Physics, 23 (33)
Physical Chemistry Chemical Physics, 23 (33)
The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumera
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::64d300a7c917ace7da4f4730789667b9
https://doi.org/10.1039/d1cp02001c
https://doi.org/10.1039/d1cp02001c
Publikováno v:
Journal of Computer-Aided Molecular Design, 36 (3)
The calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed “single topology” or “dual to
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c33cd30a98c3c4b0ad3036c3a38e3885