Zobrazeno 1 - 10 of 286 pro vyhledávání: '"R. Rieder"'
1
Akademický článek
Development of an open-source software for isomer enumeration
Autor: Salomé R. Rieder, Marina P. Oliveira, Sereina Riniker, 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
Zobrazit plný text záznamu
2
Akademický článek
Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS
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
Zobrazit plný text záznamu
4
Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set
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
Zobrazit plný text záznamu
5
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities
Autor: Emilia P. Barros, Benjamin Ries, Candide Champion, Salomé R. Rieder, Sereina Riniker
Publikováno v: Journal of Chemical Information and Modeling, 63 (6)
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding medium by a
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::49297bd27348d1481be1511f9fd1d4ad
https://hdl.handle.net/20.500.11850/606848
Zobrazit plný text záznamu
7
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules
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
Zobrazit plný text záznamu
8
Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff
Autor: Salomé R. Rieder, Benjamin Ries, Alžbeta Kubincová, Candide Champion, Emilia P. Barros, Philippe H. Hünenberger, Sereina Riniker
Publikováno v: The Journal of Chemical Physics, 157 (10)
Replica-exchange enveloping distribution sampling (RE-EDS) is a pathway-independent multistate free-energy method currently implemented in the GROMOS software package for molecular dynamics (MD) simulations. It has a high intrinsic sampling efficienc
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a92cc97447bceebd37fa2ebc8f1b644e
https://doi.org/10.1063/5.0107935
Zobrazit plný text záznamu
9
Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes
Autor: Philippe H. Hünenberger, Maurice Andrey, Marina P. Oliveira, Salomé R. Rieder, Bruno A. C. Horta, David F. Hahn, Sereina Riniker, Leyla S. Kern
Publikováno v: Journal of Chemical Theory and Computation, 16 (12)
Direct optimization against experimental condensed-phase properties concerning small organic molecules still represents the most reliable way to calibrate the empirical parameters of a force field. However, compared to a corresponding calibration aga
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::58bf0b9f7045e2797c69ab2fa1d73661
https://hdl.handle.net/20.500.11850/457688
Zobrazit plný text záznamu
10
Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies
Autor: William E. Acree, Sadra Kashefolgheta, Salomé R. Rieder, Philippe H. Hünenberger, Marina P. Oliveira, Bruno A. C. Horta
Publikováno v: Journal of Chemical Theory and Computation, 16 (12)
Experimental solvation free energies are nowadays commonly included as target properties in the validation and sometimes even in the calibration of condensed-phase force fields. However, this is often done in a nonsystematic fashion, by considering a
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7435bd467dee7137e2d980ca10b2bb84
https://pubmed.ncbi.nlm.nih.gov/33147017
Zobrazit plný text záznamu

Vyhledávací nástroje:

Upřesnit hledání

Omezení vyhledávání
Plný text Recenzováno Digitální knihovna AV ČR
Zdroje