Zobrazeno 1 - 10
of 283
pro vyhledávání: '"R. Rieder"'
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
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
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
https://hdl.handle.net/20.500.11850/606848
Autor:
Thiago P Leal, Jennifer N French-Kwawu, Mateus H Gouveia, Victor Borda, Miguel Inca-Martinez, Emily A Mason, Andrea RVR Horimoto, Douglas P Loesch, Elif I Sarihan, Mario R Cornejo-Olivas, Luis E Torres, Pilar E Mazzetti-Soler, Carlos Cosentino, Elison H Sarapura-Castro, Andrea Rivera-Valdivia, Angel C Medina, Elena M Dieguez, Víctor E Raggio, Andrés Lescano, Vitor Tumas, Vanderci Borges, Henrique B Ferraz, Carlos R Rieder, Artur Schumacher-Schuh, Bruno L Santos-Lobato, Carlos Velez-Pardo, Marlene Jimenez-Del-Rio, Francisco Lopera, Sonia Moreno, Pedro Chana-Cuevas, William Fernandez, Gonzalo Arboleda, Humberto Arboleda, Carlos E Arboleda Bustos, Dora Yearout, Maria F Lima-Costa, Eduardo Tarazona, Cyrus Zabetian, Timothy A Thornton, Timothy D O’Connor, Ignacio F Mata
Publikováno v:
medRxiv
Sex differences in Parkinson Disease (PD) risk are well-known. However, it is still unclear the role of sex chromosomes in the development and progression of PD. We performed the first X-chromosome Wide Association Study (XWAS) for PD risk in Latin A
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::611448199f677e7660d221b8a0d775d6
https://europepmc.org/articles/PMC9915833/
https://europepmc.org/articles/PMC9915833/
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
Autor:
Ana Cecília Guimarães Alves, Natalie Mary Sukow, Gabriel Adelman Cipolla, Marla Mendes, Thiago P. Leal, Maria Luiza Petzl-Erler, Ricardo Lehtonen Rodrigues Souza, Ilíada Rainha de Souza, Cesar Sanchez, Meddly Santolalla, Douglas Loesch, Michael Dean, Moara Machado, Jee-Young Moon, Robert Kaplan, Kari E. North, Scott Weiss, Mauricio L. Barreto, M. Fernanda Lima-Costa, Heinner Guio, Omar Cáceres, Carlos Padilla, Eduardo Tarazona-Santos, Ignacio F. Mata, Elena Dieguez, Víctor Raggio, Andres Lescano, Vitor Tumas, Vanderci Borges, Henrique B. Ferraz, Carlos R. Rieder, Artur Schumacher-Schuh, Bruno L. Santos-Lobato, Pedro Chana-Cuevas, William Fernandez, Gonzalo Arboleda, Humberto Arboleda, Carlos E. Arboleda-Bustos, Timothy D. O’Connor, Marcia Holsbach Beltrame, Victor Borda
Publikováno v:
Frontiers in Genetics
Frontiers in Genetics, Vol 12 (2021)
Frontiers in Genetics, Vol 12 (2021)
In adulthood, the ability to digest lactose, the main sugar present in milk of mammals, is a phenotype (lactase persistence) observed in historically herder populations, mainly Northern Europeans, Eastern Africans, and Middle Eastern nomads. As the
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
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
https://hdl.handle.net/20.500.11850/457688
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