Learning Universal Representations of Intermolecular Interactions with ATOMICA

A high-performance, pure Rust toolkit for standardizing and preparing biomolecular systems (proteins & nucleic acids). It heals missing atoms, resolves protonation states, adds solvation, and unifies topologies to forge simulation-ready structures.

Nucleic and amino acid primitive types

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

An analysis of a new experimentally-derived nucleic acid binding chemical library

使用 OCR + 正则表达式实现核酸检测截图的自动校验，复现复旦大学博士生的代码

A Python application to find and classify tetrads and quadruplexes in DNA/RNA 3D structures

Using data from PDBePISA with the convenience of Python and Jupyter.

🧬🦠🧪 [research][wip] Library for working with DNA, RNA, and etc acids

Align short RNA seqeuncing reads to determine the length of of overhang

Geometry faithful 2D RNA visualization

Analysis workflow for smallRNA sequenced data

Similarity Score Matrix and HeatMap for Nucleic and Amino acid K-mers

A Generalized Algorithm for Coarse-Graining Molecular Dynamics Simulations with Boltzmann parametrization

Python application to compare ssNa secondary structures

Construct atomistic (AA) model from Three-Interaction-Site (TIS) coarse-grained model of RNA/DNA

A high-performance, pure Rust library for automated DREIDING force field parameterization. It orchestrates structure repair, topology perception, and partial atomic charge calculation to produce simulation-ready inputs for both biological macromolecules and arbitrary chemical systems.

Remove duplicated protein/nucleic acid sequences, keeping the first occurrence.

AnnotationDb for post-transcriptional modifications (Mmusculus.mm10)

A high-performance, pure Rust library for full-atom protein side-chain packing using the DREIDING force field, Goldstein+Split DEE, and tree-decomposition DP—with native protein–ligand and protein–nucleic acid interface support.