biomolecular-md-workflow

仓库创建 2026年7月6日最近提交 21 天前SkillHot 收录 20 天前

▸ 精选理由

强调以问题驱动、证据为准的建模决策流程，适合研究与验证场景。

▸ 风险提示

可能需安装外部生物信息学软件并使用大量计算资源

这个 Skill 做什么

为蛋白-配体对接与分子动力学提供可辩护的全过程工作流指导。

帮你把蛋白-配体对接和分子动力学（MD）的整个流程有理有据地规划、运行和复核。适合做对接位姿审查、对接到MD的验证、膜蛋白或多聚体建模，以及比较突变/重对接/MD结果时用。特别强调先确定要支持的生物学结论再选方法，避免盲目跑生产级 MD，关注生物装配、质子化、力场覆盖和起始位姿的可靠性。

▸ 展开 SKILL.md 英文原文

Plan, run, review, and report defensible biomolecular docking and molecular dynamics workflows. Use for protein-ligand docking, docking-pose review, docking-to-MD validation, protein-only MD, membrane-protein MD, multimer modeling, mutation/redocking/MD comparisons, ligand or lipid parameterization decisions, trajectory analysis, free-energy escalation, and cases where MD should be avoided or caveated because the biological assembly, membrane state, protonation, ligand parameters, or starting pose is not reliable.

研究检索生物建模对接+MD工作流通用

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帮我安装这个 skill：https://raw.githubusercontent.com/dailycafi/biomolecular-md-workflow/main/SKILL.md

或 curl 直取 SKILL.md

curl -fsSL "https://raw.githubusercontent.com/dailycafi/biomolecular-md-workflow/main/SKILL.md"

SKILL.MD 节选查看完整文件 ↗

# Biomolecular MD Workflow

## Core Rule

Treat biomolecular modeling as a question-driven evidence workflow, not as a fixed docking-then-MD recipe. First decide what claim the computation is supposed to support, then choose the least overclaimed method that can test it. Do not start production MD until the biological assembly, chemical states, force-field coverage, environment, and starting pose/model are defensible.

For detailed protocols and edge cases, read the relevant reference file:

- [references/methodology.md](references/methodology.md): overall method routing, docking, MD, membrane systems, mutations, and free-energy escalation.
- [references/quality_gates.md](references/quality_

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