Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.4c00990
Abstract: The need for short time steps currently limits routine atomistic molecular dynamics (MD) simulations to the microsecond time scale. For long time steps, the numerical integration of the equations of motion becomes unstable, resulting in… read more here.
Keywords: time; sampling molecular; water; dynamics simulations ... See more keywords
High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.5c00163
Abstract: A new module for quantum mechanical/molecular mechanical (QM/MM) calculations is implemented in a molecular dynamics (MD) program, SPDYN in GENESIS, interfaced with an electronic structure program, QSimulate-QM. The periodic boundary condition (PBC) in QM/MM simulation… read more here.
Keywords: sampling molecular; high performance; molecular dynamics; performance enhanced ... See more keywords
Studying Disease-Associated UBE3A Missense Variants Using Enhanced Sampling Molecular Simulations
Sign Up to like & getrecommendations! Published in 2022 at "ACS Omega"
DOI: 10.1021/acsomega.2c00959
Abstract: Missense variants in UBE3A underlie neurodevelopmental conditions such as Angelman Syndrome and Autism Spectrum Disorder, but the underlying molecular pathological consequences on protein folding and function are poorly understood. Here, we report a novel, maternally… read more here.
Keywords: sampling molecular; enhanced sampling; missense; missense variants ... See more keywords
Sampling molecular conformations and dynamics in a multiuser virtual reality framework
Sign Up to like & getrecommendations! Published in 2018 at "Science Advances"
DOI: 10.1126/sciadv.aat2731
Abstract: VR combined with cloud computing enables surgical manipulation of real-time molecular simulations, accelerating 3D research tasks. We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic… read more here.
Keywords: sampling molecular; framework; multiuser virtual; virtual reality ... See more keywords
Usefulness of salivary sampling for the molecular detection of a genetic variant associated with bipolar disorders
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Public Health Research"
DOI: 10.1177/22799036221146915
Abstract: Under certain conditions, the hyperthymic temperament traits associated with an increased risk of developing bipolar disorders may in fact produce adaptive responses. The purpose of this study is to see if the type of biological… read more here.
Keywords: sampling molecular; usefulness salivary; salivary sampling; bipolar disorders ... See more keywords
The Interaction of Factor Xa and IXa with Non-Activated Antithrombin in Michaelis Complex: Insights from Enhanced-Sampling Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2023 at "Biomolecules"
DOI: 10.3390/biom13050795
Abstract: The interaction between coagulation factors Xa and IXa and the activated state of their inhibitor, antithrombin (AT),have been investigated using X-ray diffraction studies. However, only mutagenesis data are available for non-activated AT. Our aim was… read more here.
Keywords: dynamics simulations; sampling molecular; molecular dynamics; interaction factor ... See more keywords
Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms23147558
Abstract: (1) Background: Virtual screening campaigns require target structures in which the pockets are properly arranged for binding. Without these, MD simulations can be used to relax the available target structures, optimizing the fine architecture of… read more here.
Keywords: extensive sampling; protein structures; sampling molecular; virtual screening ... See more keywords