The molecular modeling toolkit: A new approach to molecular simulations

By Konrad Hinsen. Journal of Computational Chemistry, 2000

323 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/27b118f71f2ca1b66e58363b372dc489cd1e30fe

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In Materials Chemistry

In Molecular Biology

In Spectroscopy

Citations in the corpus

Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, methodology): “As noted in the introduction, a number of previously implemented software solutions (including multiple web-servers [10-12,45] and standalone software packages [13-15,46]) offer single structure NMA or MD analysis.”
Dynamics of proteins in solution (2019, methodology): “…motions is a normal mode analysis aiming at the low-frequency Brownian modes (Hinsen, 1998; Doruker et al., 2000; Hinsen et al., 2000; Cui and Bahar, 2006), as implemented in open-source software packages such as the molecular modeling toolkit MMTK (Hinsen, 2000) or ProDy (Bakan et al., 2011).”
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. (2004, methodology): “Similar, scripting-language based designs have been used successfully in other related applications such as the molecular modeling tool kit (MMTK) [21] or the Bioperl toolkit [22].”
MPI for Python: Performance improvements and MPI-2 extensions (2008, background): “Following the aforementioned trends, some researchers have taken advantage of Python for writing the high-level parts of large-scale, massively parallel scientific applications and driving simulations in parallel architectures [12,13], while others have tried to make available the benefits of parall”
Biopython: freely available Python tools for computational molecular biology and bioinformatics (2009, methodology): “Python has even been used in the numerically demanding field of molecular dynamics (Hinsen, 2000).”
The Bio3D packages for structural bioinformatics (2020, methodology): “A number of previously implemented software solutions (including multiple web servers 31 – 35 and standalone software packages 36 – 42 ) offer related solutions including single structure NMA, MD or protein structure-based network analysis.”
Gradients are Not All You Need (2021, background): “…al., 2018, Gradu et al., 2021, Freeman et al., 2021], graphics [Li et al., 2018, Kato et al., 2020], molecular dynamics [Schoenholz and Cubuk, 2020, Hinsen, 2000], differentiating though optimization procedures [Maclaurin, 2016], weather simulators [Bischof et al., 1996], and nuclear fusion…”