Discovery of Novel and Potent InhA Inhibitors By an
            <i>In Silico</i>
            Screening and Pharmacokinetic Prediction

Hanwarinroj, Chayanin; Phusi, Naruedon; Kamsri, Bundit; Kamsri, Pharit; Punkvang, Auradee; Ketrat, Sombat; Saparpakorn, Patchreenart; Hannongbua, Supa; Suttisintong, Khomson; Kittakoop, Prasat; Spencer, James; Mulholland, Adrian J.; Pungpo, Pornpan

doi:10.4155/fmc-2021-0348

Cited by 4 publications

(2 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The waterswap application was developed to compute absolute binding free energies of small molecules to proteins using a Gibbs-Ensemble methodology with Monte Carlo sampling. [1][2][3] This approach was later extended to ligandswap and proteinswap, providing Sire converts this to BioSimSpace, which is used to parameterise and solvate the molecule. Sire converts the result to OpenMM, which is used to perform GPU-accelerated molecular dynamics.…”

Section: Scientific Applications Developed With Sirementioning

confidence: 99%

See 1 more Smart Citation

Sire: An Interoperability Engine for Prototyping Algorithms and Exchanging Information Between Molecular Simulation Programs

Woods,

Hedges,

Mulholland

et al. 2024

Preprint

View full text Add to dashboard Cite

Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterise molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire’s molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber and AmberTools, for automated molecular parameterisation and running of molecular dynamics, metadynamics and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit and combine molecular information from multiple sources, and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https://try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company.

show abstract

Section: Scientific Applications Developed With Sirementioning

confidence: 99%

“…sire would be the "parent" of other programs. Software developed using sire includes waterswap [1][2][3] , quantomm 4 , nautilus 5 , somd 6 , FESetup 7 and most notably BioSimSpace 8,9 . Commercially, sire is embedded in Flare produced by Cresset [10][11][12] and within the drug discovery pipelines used by Exscientia.ai 13 .…”

Section: Introduction and Featuresmentioning

confidence: 99%