.png){kind=icon}
返回
Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs
.png){kind=icon}
OA
AI
DOI：10.1063/5.0200458.png)
.png){kind=icon}
原文求助.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
Sire is a Python/C++ library that is used both to 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, parameterize 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 parameterization and the 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.
Keyword:
BLINDED PREDICTIONS
BINDING-ENERGIES
DYNAMICS
DISCOVERY
FIELD
期刊
IF:
3.1
论文数:
7.2W
被引数:
23.2W
机构
引用论文
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics TrajectoriesMDTraj: 用于分析分子动力学轨迹的现代开放库.png)
BIOPHYSICAL JOURNAL
OAAI
BIOPHYSICAL JOURNALIF3.1
OAAI分享收藏Metabolism and hydrophilicity of the polarised 'Janus face' all-cis tetrafluorocyclohexyl ring, a candidate motif for drug discovery极化的 “janus脸” 全顺四氟环己基环的代谢和亲水性，这是药物发现的候选基序CHEMICAL SCIENCEOAAI
CHEMICAL SCIENCEIF7.4
OAAI分享收藏SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules微笑，一种化学语言和信息系统。1.介绍方法和编码规则
PREAI
分享收藏Data-driven generation of perturbation networks for relative binding free energy calculationsDIGITAL DISCOVERYOAAI
DIGITAL DISCOVERYIF5.6
OAAI分享收藏
查看更多内容