3dmol

Utilities for analyzing and reporting results from Smina virtual screens

3D visualization of chemicals using 3DMol.js.

Molecular structure visualizations with 3Dmol.js in Power BI

🤗 Hugging Face space for gnina-torch 🔥

Local CADD docking platform with 3D box manipulation, automated pocket prediction, AutoDock Vina docking, and interactive result visualization.

An Antigravity 2.0 IDE experiment: visualizing heat effects on human proteins. Educational, not clinical.

Paste a SMILES string, see the molecule: instant 2D structure, spinnable 3D model, and molecular formula and weight, all in your browser.

An AI-powered protein engineering suite using Google ADK and Gemini 2.5. Orchestrates specialized multi-agent workflows to query AlphaFold DB, calculate structural mutation dynamics, and render modified 3D proteins in real time.

All-in-one web platform for protein pocket prediction, ligand docking, ADMET profiling, and MM-GBSA rescoring — powered by P2Rank, AutoDock Vina, RDKit, and OpenMM.

IDPP Studio — Windows 可视化 NEB 初猜路径生成器（pymatgen IDPP + 3Dmol.js + pywebview）

Graph-based Protein-Peptide Interaction Predictor. Reranking candidates using ESM-2 embeddings and Graph Neural Networks (GNN) on PROPEDIA data.

Browser-native molecular trajectory viewer with force coloring, atom measurements, and Extended XYZ / VASP parsers. Extracted from simviz.io.

Independent open-source WebGL trajectory viewer for the GPUMD ecosystem

Headless molecular visualization and structural biophysics skill for AI agents. Generates publication renders, AlphaFold pLDDT maps, binding pockets, alignments, and web dashboards via PyMOL and OSMesa.

VASP XDATCAR/OUTCAR 轨迹可视化与收敛分析工作台 | 3Dmol.js 交互式 3D + 力/能量曲线 + 一键导出 GIF (PySide6)

Custom Claude skills by tutoringwithsruthi

Diff two crystal structures, surface every change (displacement, bonds, coordination, cell, symmetry), and read an LLM narrative explaining whether the DFT relaxation looks reasonable. CIF / POSCAR / extxyz.

Chemistry project created for school competition

🔬 FixAtoms Studio — 本地离线原子结构固定工具。基于 PySide6 (Qt 6) + ASE + 3Dmol.js，支持 CIF / POSCAR / XSD 读取，可视化固定原子并导出 VASP Selective dynamics POSCAR；内置 118 元素周期表、六个晶胞标准视图、正交/透视投影与深度雾化。

基于 PySide6 + 3Dmol.js + Matplotlib 的 VASP 态密度（TDOS / PDOS）与晶体结构可视化桌面工作台：iOS / macOS 风格界面，六页面，支持带中心计算、高斯圆滑与图片导出。