Tool · Desktop · Windows · Single-file

AptaFold

适配体二级结构预测

DNA aptamer secondary-structure prediction with explicit Na⁺ / Mg²⁺ / K⁺ / Ca²⁺ / temperature inputs, motif-aware constraints, and G-quadruplex detection & rendering — built to replace m-fold / UNAFold for routine SELEX lab use.

面向 DNA 适配体的二级结构预测工具，显式考虑 Na⁺ / Mg²⁺ / K⁺ / Ca²⁺ 与温度，支持基序约束、G-四链体识别与可视化，目标是在 SELEX 实验室日常工作中替代 m-fold / UNAFold。

Download for Windows v0.6.7 · 114 MB · single-file .exe Download for macOS v0.6.7 · 58 MB · .dmg

v0.6.7 · MIT license · Windows: single-file .exe · macOS: .dmg

macOS build is compiled without the numba JIT — that's why it's a smaller download (58 MB vs 114 MB on Windows); folding of large inputs may run a little slower. · macOS 版未编译 numba 加速,因此体积更小(58 MB,Windows 为 114 MB);处理大输入时折叠速度可能略慢。

/ Introduction · 介绍

What it does.这个工具能做什么。

AptaFold predicts DNA (and RNA) secondary structure with the salt and temperature conditions actually used in aptamer assays. It pairs ViennaRNA's monovalent salt correction with a per-loop divalent callback for Mg²⁺ and Ca²⁺, and adds a G-quadruplex channel-binding term for K⁺ / Na⁺. The desktop GUI exposes every parameter you'd normally hide in a CLI, with motif-aware constraints (Loose-scaffold SELEX mode) and a layered G-quadruplex cartoon view for the topology you'd otherwise read off a paper.

AptaFold 针对适配体实验中真正使用的盐浓度和温度条件，预测 DNA（也支持 RNA）二级结构。它在 ViennaRNA 的一价盐校正之外，加入了 Mg²⁺ 与 Ca²⁺ 的每环二价钙镁回调，以及 K⁺ / Na⁺ 的 G-四链体通道结合项。桌面 GUI 将所有 CLI 参数都直接展示出来，支持基序约束（SELEX Loose-scaffold 模式）和分层 G-四链体卡通视图，让拓扑信息一目了然。

Four-cation aware folding

四种阳离子的协同建模

Explicit Na⁺, Mg²⁺, K⁺, Ca²⁺ inputs with temperature — the only open tool we know of that touches Mg²⁺-vs-Ca²⁺ for DNA aptamers.

显式输入 Na⁺、Mg²⁺、K⁺、Ca²⁺ 与温度——目前已知唯一在 DNA 适配体上处理 Mg²⁺-vs-Ca²⁺ 差异的开源工具。
G-quadruplex detection & cartoon

G-四链体识别与可视化

Detects G-tract motifs, scores topology under K⁺ / Na⁺ channel binding, and renders both axial (top-down tetrad) and side (layer-diagram) views via a DrawTetrado-style painter's algorithm. The main fold viewer also auto-switches to 3D when a G4 is found, with a Flat ↔ 3D toggle.

识别 G-富集序列，按 K⁺ / Na⁺ 通道结合给出拓扑评分，绘制俯视（四联体）与侧视（层图）两种卡通图，采用类似 DrawTetrado 的画家算法。主折叠视图检测到 G4 时自动切换为 3D 视图，并提供 Flat ↔ 3D 切换按钮。
Four interchangeable engines

四套可切换引擎

seqfold (pure-Python fallback), ViennaRNA (industry default, monovalent salt), ViennaRNA+Mg²⁺ (experimental Mg²⁺ callback), and 4cations DP (full four-cation experimental engine).

seqfold（纯 Python 兜底）、ViennaRNA（业内默认，仅一价盐）、ViennaRNA+Mg²⁺（实验性 Mg²⁺ 回调）、4cations DP（完整四阳离子实验性引擎）。
Suboptimal-fold exploration

次优结构探索

Wuchty-style enumeration of folds within ΔE of the MFE, with a coverage cap and "show 10/20/30" controls — useful when the MFE alone hides the relevant conformation.

Wuchty 风格枚举 MFE 上 ΔE 内的所有次优结构，并提供覆盖率上限与「显示 10/20/30 条」控件——MFE 单独不足时尤其有用。
Motif-aware constraints

基序约束

"Loose scaffold (SELEX)" mode keeps the known fixed primer-binding region as scaffold and lets the random N region fold freely — a one-click constraint that matches how SELEX libraries are actually designed.

「Loose scaffold (SELEX)」模式保留固定引物结合区作为支架，只让随机 N 区自由折叠——一键应用，匹配 SELEX 文库的真实设计。
Multi-format export

多格式导出

PDF, PNG, SVG, JSON, CSV, and PPTX. Also includes a batch mode for running many sequences at once through the same parameter set.

支持 PDF、PNG、SVG、JSON、CSV、PPTX 导出。还提供批处理模式：一组参数批量处理多条序列。

/ Engines · 引擎一览

seqfoldPure-Python fallback. No salt model. Useful when ViennaRNA isn't available. 纯 Python 兜底，无盐模型。ViennaRNA 不可用时使用。
ViennaRNAIndustry-default thermodynamic engine with Lai et al. 2023 monovalent salt correction. 业内默认热力学引擎，Lai 等 2023 一价盐校正。
ViennaRNA+Mg²⁺Experimental: ViennaRNA + per-loop Mg²⁺ callback (uncalibrated). 实验性：ViennaRNA + 每环 Mg²⁺ 回调（未校准）。
4cations DPExperimental: full four-cation dynamic-programming engine (uncalibrated). 实验性：完整四阳离子动态规划引擎（未校准）。

/ Usage · 使用方式

How to use it.使用流程。

AptaFold ships as a single-file Windows executable (~114 MB). Download it, double-click — no installer, no extraction, no admin rights.

AptaFold 以单文件 Windows 可执行程序形式发布（约 114 MB）。下载后双击即可运行——无需安装、无需解压、无需管理员权限。

01

Download & launch

下载并启动

Click the download button above (AptaFold-0.6.7-onefile.exe, 114 MB). Just double-click the downloaded EXE — it's a self-contained single-file build, no install step, no folder to manage. The main window opens straight up and shows the sequence box, ionic-condition sliders, engine picker, and fold buttons. First-run takes a couple of extra seconds while the bundle unpacks to a temp folder.

点击上方下载按钮（AptaFold-0.6.7-onefile.exe，114 MB）。直接双击下载到的 EXE 即可——单文件自包含构建，不用安装、不用管理子目录。主窗口直接弹出，显示序列输入框、离子浓度滑块、引擎选择器与折叠按钮。首次启动会多花几秒钟解压临时文件，之后再次启动会更快。

Screenshot · 01-main-window.png

Fig. 01 — Main window · 主窗口（输入区与条件区）
02

Enter sequence & ionic conditions

输入序列与离子条件

Type or paste the sequence (ATCG / AUCG). Set [Na⁺], [Mg²⁺], [K⁺], [Ca²⁺] in mol/L and the temperature in °C — defaults match a common SELEX selection buffer. Choose an engine (default 4cations), and tick options: G-quad scoring, Suboptimals within ΔE, Loose scaffold (SELEX) for motif-aware constraints.

输入或粘贴序列（ATCG / AUCG）。设置 [Na⁺]、[Mg²⁺]、[K⁺]、[Ca²⁺]（mol/L）与温度（°C），默认值对应常见的 SELEX 筛选缓冲液。选择引擎（默认 4cations），并按需勾选：G-quad 评分、ΔE 范围内的次优结构、SELEX 的 Loose scaffold 基序约束。
03

Fold & read the result

折叠并查看结果

Click Fold. The result panel renders the secondary structure inline — base-pair stems drawn with Watson–Crick H-bonds in red, with position numbers, 5′ / 3′ termini, and ΔG values printed alongside each fold. You can Re-fold after changing conditions without reloading anything.

点击 Fold，结果面板会直接绘制二级结构——茎区的 Watson–Crick 氢键用红色短线标出，配有位置编号、5′/3′ 末端标记，并显示每条结构的 ΔG。改变条件后点击 Re-fold 即可重算，无需重新输入。

Screenshot · 02-fold-hairpin.png

Fig. 02 — Fold render · 二级结构示例（茎-环-内 bulge-小发卡）

When the predicted fold contains a G-tetrad, AptaFold detects the G4 and defaults the result viewer to the 3D oblique-cube layout — the four G-tracts stack as parallel rails so the tetrad geometry reads at a glance. Click the Flat ↔ 3D toggle in the bottom-left of the result panel to switch to the conventional flat secondary-structure layout (and back). The toggle is sticky per fold, so a re-fold preserves your view choice.

当折叠结果包含 G-四链体时，AptaFold 会自动识别并将结果默认切换为 3D 斜方块视图——四条 G 段作为平行轨道并排堆叠，四联体几何一目了然。点击结果面板左下角的 Flat ↔ 3D 切换按钮可以回到经典的平面二级结构布局（再点回去）。切换状态按 fold 记忆，重新折叠后视图选择保留。

Fig. 03 — Same G4 fold, flat (left) vs 3D (right) · 同一条 G-四链体折叠的 Flat / 3D 视图
04

G-quadruplex detail (if found)

查看 G-四链体细节（若检测到）

If G-tract motifs are detected (and G-quad scoring is on), the G-quad… button activates. Open it for a layered cartoon: axial view shows the tetrad from above with the central cation, side view shows tetrad stacking with propeller / lateral / diagonal loops drawn as external arcs. Each view exports as PNG / SVG / JSON / CSV.

检测到 G 段且开启了 G-quad 评分时，G-quad… 按钮会激活。打开后会显示分层卡通图：俯视图显示四联体与中心阳离子，侧视图显示四联体堆叠及螺旋桨/侧/对角环（绘为外接弧线）。每个视图都可导出 PNG / SVG / JSON / CSV。

Fig. 03/04 — G-quadruplex side & axial · 侧视与俯视
05

Export, or run a batch

导出，或运行批处理

Export… writes the current fold (or the whole suboptimal set) as PDF, PNG, SVG, JSON, CSV, or PPTX. For many sequences at once, switch the Input source from Manual sequence to a CSV / Excel / Liu-Lab Aptamer Analysis output — AptaFold runs the same parameter set across all rows and exports per-sequence files.

点击 Export… 将当前结构（或全部次优解）保存为 PDF / PNG / SVG / JSON / CSV / PPTX。批量处理多条序列时，把输入源从 Manual sequence 切换到 CSV / Excel / 刘实验室 Aptamer Analysis 输出文件——AptaFold 会按同一组参数批量运行并按序列分别导出。

/ Disclaimer · 声明

Things to know.使用前请阅读。

Engineering approximation, not calibrated physical chemistry.

是工程近似，不是已校准的物理化学

The four-cation engine combines published trends (ViennaRNA monovalent salt correction, Tan–Chen tightly-bound-ion ideas, G-quadruplex channel-binding) into a single model. It is intentionally conservative and uncalibrated — use the output as a trend check and starting hypothesis, not as a quantitative T_m prediction.

四阳离子引擎把已发表的趋势（ViennaRNA 一价盐校正、Tan–Chen 紧束缚离子模型、G-四链体通道结合）合并到一个模型里。它是有意保守且未经校准的——请将其结果作为趋势检查与起点假设，不要当作量化 T_m 预测。
Mg²⁺ / Ca²⁺ effects are experimental.

Mg²⁺ / Ca²⁺ 项目前是实验性的

No open folding tool natively handles divalent cations — ViennaRNA's salt correction is monovalent-only. AptaFold's ViennaRNA+Mg²⁺ and 4cations DP engines are experimental and pending the wet-lab T_m / ITC calibration described in the project's EXPERIMENT_PLAN.md.

目前没有开源折叠工具原生支持二价阳离子——ViennaRNA 的盐校正只针对一价盐。AptaFold 中的 ViennaRNA+Mg²⁺ 与 4cations DP 引擎属于实验性，正在等待项目 EXPERIMENT_PLAN.md 中描述的湿实验 T_m / ITC 校准。
Local processing, no telemetry.

本地处理，无遥测

AptaFold makes no network calls. Sequence input, folding, rendering, and exports all run locally. There is no auto-update check, no telemetry, no analytics.

AptaFold 不发起任何网络请求。序列输入、折叠、渲染与导出全部本地运行。无自动更新检查、无遥测、无统计上报。
MIT license · academic & non-commercial use.

MIT 许可 · 学术与非商业用途

AptaFold is released under the MIT license. Free for academic research, teaching, and personal use. ViennaRNA itself ships under its own permissive licence — see the bundled licenses/ notice.

AptaFold 以 MIT 许可发布，免费用于学术研究、教学与个人使用。ViennaRNA 本身使用各自的开源许可证——详见随软件分发的 licenses/ 说明。
Provided as-is, without warranty.

不提供任何形式的担保

Fold output is best-effort. Validate critical findings with independent methods — m-fold / UNAFold for Mg²⁺ comparison, CD / UV-melting for G-quadruplex topology. Bug reports: [email protected].

折叠输出尽力而为。关键结论请用独立方法复核——m-fold / UNAFold 做 Mg²⁺ 对照，CD / UV-melting 验证 G-四链体拓扑。Bug 与反馈请发到 [email protected]。
Cite if used in publications.

论文使用请引用

If AptaFold contributed to a published study, please cite: Zhang X. AptaFold (dna-fold), v0.6.7, Liu Lab, University of Waterloo, 2026. zxiaohan.com/research/tools/aptafold.

若 AptaFold 对已发表的研究有帮助，烦请按上述格式引用。

/ Acknowledgments · 致谢

Built on prior work.站在前人工作之上。

Developed in the Bionanotechnology & Interfaces Laboratory at the University of Waterloo, led by Prof. Juewen Liu. AptaFold's identity, four-cation model, and G-quadruplex visualization grew out of the lab's daily SELEX / aptamer-folding needs — and out of the realization that no open tool actually handles the ionic conditions our buffers use.

本工具在加拿大滑铁卢大学刘珏文教授的 Bionanotechnology & Interfaces Laboratory 完成。AptaFold 的视觉系统、四阳离子模型与 G-四链体可视化，源于实验室日常 SELEX / 适配体折叠的实际需求——以及"没有任何开源工具真正考虑我们缓冲液里的离子条件"这个事实。

Prof. Juewen Liu

Training data & support · 训练数据与支持

Professor of Chemistry at the University of Waterloo. Tier 1 Canada Research Chair in Biosensors & Bionanotechnology. Provided the invaluable wet-lab training data and ongoing support that made the four-cation calibration possible.
Xiaohan Zhang

Author · Development · Formulas · ML · 作者 · 开发 · 公式 · 机器学习

Postdoctoral researcher at the University of Waterloo under Prof. Juewen Liu. Main developer — designed and implemented the engine, derived the formulas, tuned the parameters, and built the machine-learning components of the four-cation model.
Yuanli Li

Data collection & cleaning · 数据收集与清洗

Third-year undergraduate in the Materials Nanoscience joint program (Beijing Jiaotong University × University of Waterloo). Built the training dataset — collected the literature and wet-lab measurements, cleaned them into the calibration-ready form used by the four-cation engine.

Standing on prior work. AptaFold also builds on the following projects and frameworks:

同时致敬前人工作。AptaFold 还建立在以下项目与理论框架之上：

ViennaRNA · Lorenz, Hofacker, et al.

ViennaRNA 团队

The industry-default RNA folding engine. AptaFold's default and +Mg²⁺ engines are both layered on top of ViennaRNA, including the Lai et al. 2023 monovalent salt correction.

业内默认的 RNA 折叠引擎。AptaFold 的默认引擎与 +Mg²⁺ 引擎都建立在 ViennaRNA 之上，包含 Lai 等 2023 的一价盐校正。
DrawTetrado · Zok et al. 2022

G-四链体绘图参考

AptaFold's oblique G4 cube uses a painter's-algorithm depth ordering and propeller-loop arc style directly inspired by DrawTetrado (Zok et al., Bioinformatics 38:3835, 2022) — the purpose-built G-quadruplex layer-diagram tool that nailed the visual conventions.

AptaFold 的 G4 立方体斜视图借鉴了 DrawTetrado（Zok 等，Bioinformatics 38:3835, 2022）的画家算法图层顺序与螺旋桨环弧线风格——这套用于 G-四链体层图的工具确立了相关的可视化惯例。
Tan, Chen et al. — tightly-bound-ion model

紧束缚离子模型

The per-loop divalent callback design draws on the Tan–Chen tightly-bound-ion framework — the most physically principled treatment of Mg²⁺ in nucleic-acid folding, even though it had never been integrated into a distributable folding tool before.

每环二价回调的设计借鉴了 Tan–Chen 紧束缚离子框架——这是核酸折叠中 Mg²⁺ 在物理原理上最合理的处理方法，但在此之前从未被整合进可分发的折叠工具。

Open-source libraries. AptaFold stands on the work of these projects — thanks to their maintainers:

开源依赖。AptaFold 依赖以下开源项目，感谢各位维护者：

ViennaRNA
seqfold
PySide6
NumPy
matplotlib
python-pptx
openpyxl
pypdf
xlrd
numba

/ Also in the toolkit · 工具集

AptaFold

What it does.这个工具能做什么。

Four-cation aware folding

G-quadruplex detection & cartoon

Four interchangeable engines

Suboptimal-fold exploration

Motif-aware constraints

Multi-format export

How to use it.使用流程。

Download & launch

Enter sequence & ionic conditions

Fold & read the result

G-quadruplex detail (if found)

Export, or run a batch

Things to know.使用前请阅读。

Engineering approximation, not calibrated physical chemistry.

Mg²⁺ / Ca²⁺ effects are experimental.

Local processing, no telemetry.

MIT license · academic & non-commercial use.

Provided as-is, without warranty.

Cite if used in publications.

Built on prior work.站在前人工作之上。

Prof. Juewen Liu

Xiaohan Zhang

Yuanli Li

ViennaRNA · Lorenz, Hofacker, et al.

DrawTetrado · Zok et al. 2022

Tan, Chen et al. — tightly-bound-ion model

Other tools.同系列工具。

Aptamer Analysis Tool

Kd Fitting Tool

Structural Family Classification

K_d Fitting Tool