Dev tools · alternatives · 2026

24 alternatives to Open-source protein and ligand viewer

I just published an open-source protein and ligand viewer. Goal: fast and easy-to-use. Long-term: It's a platform for docking and molecular dynamics. The basic functionality for viewing and inspecting work. I'm currently working on Coot-like electron-density viewing. I'm gradually splitting it into standalone libs, published to crates.io. Some are up already, others are integrated, and will be split off when sufficiently mature and decoupled. Uses parallel execution when able, through thread pools (Rayon), CPU SIMD and Cuda. The default control scheme is non-standard, unless you play video…

This open-source protein and ligand viewer enables researchers to visualize and inspect molecular structures with an emphasis on speed and ease of use. Built as a foundation for future docking and molecular dynamics… Below are 24 products that do a similar job, ranked by how close each is in meaning and then by launch-day votes.

1
PlasCAD: Open-source plasmid editor▲101
Hey! This is an open source plasmid and vector (Short, often circular segments of DNA) editor, with features related to primer quality checks, PCR cloning, and protein analysis. I plan to add more restriction-enzyme-based features in the near future. It has some extras like a solution-mixing helper, automatic feature annotation. From a technical standpoint, this is a standalone binary written using the EGUI library in rust. A project goal is performance, with small memory footprint, and small application and file sizes. This is a continuous work-in-progress, and I'm open to any and all…
2024 · github.com · its alternatives →
2
Parqeye – A CLI tool to visualize and inspect Parquet files▲167
I built a Rust-based CLI/terminal UI for inspecting Parquet files—data, metadata, and row-group-level structure—right from the terminal. If someone sent me a Parquet file, I used to open DuckDB or Polars just to see what was inside. Now I can do it with one command. Repo: https://github.com/kaushiksrini/parqeye
Nov 2025 · github.com · its alternatives →
3
HelixDB – Open-source vector-graph database for AI applications (Rust)▲237
Hey HN, we want to share HelixDB (https://github.com/HelixDB/helix-db/), a project a college friend and I are working on. It’s a new database that natively intertwines graph and vector types, without sacrificing performance. It’s written in Rust and our initial focus is on supporting RAG. Here’s a video runthrough: https://screen.studio/share/szgQu3yq. Why a hybrid? Vector databases are useful for similarity queries, while graph databases are useful for relationship queries. Each stores data in a way that’s best for its main type of query (e.g.…
2025 · github.com · its alternatives →
4
An open-source implementation of AlphaFold3▲314
Hi HN - we’re the founders of Ligo Biosciences and are excited to share an open-source implementation of AlphaFold3, the frontier model for protein structure prediction. Google DeepMind and their new startup Isomorphic Labs, are expanding into drug discovery. They developed AlphaFold3 as their model to accelerate drug discovery and create demand from big pharma. They already signed Novartis and Eli Lilly for $3 billion - Google’s becoming a pharma company! (https://www.isomorphiclabs.com/articles/isomorphic-labs-kick...) AlphaFold3 is a biomolecular structure prediction…
2024 · github.com · its alternatives →
5
I wrote a tool in Rust for tracking all allocations in a Linux process▲113
allocscope - a memory tracking tool. Contribute to matt-kimball/allocscope development by creating an account on GitHub.
2023 · github.com · its alternatives →
6
HelixDB▲105
An open-source OLTP graph-vector database built in Rust.
Feb 2026 · helix-db.com · its alternatives →
7
I made a crate for creating interactive chord diagrams in Rust▲51
2020 · datacrayon.com · its alternatives →
8
I made an open-source Rust program for memory-efficient genomics▲17
My cofounder and I run a startup in oncology, where we handle cancer genomics data. It occurred to me that, thanks to a recent complexity theory result, there's a clever way to run bioinformatics algorithms using far less RAM. I built this Rust engine for running whole-genome workloads in under 100MB of RAM. Runtime is a little longer as a result - O(TlogT) instead of O(T). But it should enable whole-genome analytics on consumer-grade hardware.
Nov 2025 · github.com · its alternatives →
9
a Rust ray tracer that runs on any GPU – even in the browser▲95
I’ve been experimenting with Rust lately and wanted a project that would help me explore some of its lower-level and performance-oriented features. Inspired by Sebastian Lague’s videos, I decided to implement my own ray tracer from scratch. The initial goal was just to render a simple 3D scene in the browser at a reasonable frame rate. It evolved into a small renderer that can: • Run locally or on the web using wgpu and WebAssembly • Perform mesh rendering with a Bounding Volume Hierarchy (BVH) for acceleration • Simulate both direct and indirect illumination for photorealistic results • Be…
Nov 2025 · github.com · its alternatives →
10
Horizon – GPU-accelerated infinite-canvas terminal in Rust▲84
Tabs, splits, and tmux work fine until you have several projects open with logs, tests, and long-running shells. I kept rebuilding context instead of resuming work. Horizon puts shells on an infinite canvas. You can arrange them into workspaces and reopen later with layout, scrollback, and history intact. Built in 3 days with Claude/Codex, dogfooding the workflow as I went. Feedback and contributions welcome.
Mar 2026 · github.com · its alternatives →
11
OpenDataDiscovery▲105
First open-source data discovery and observability platform
2022 · opendatadiscovery.org · its alternatives →
12
Python library for embedding large graphs (Written in Rust)▲84
Python library for embedding large graphs in 2D space, using force-directed layouts. - H4kor/graph-force
2022 · github.com · its alternatives →
13IB
I built a biological network visualization tool▲39
I've been working on nodes.bio - an interactive tool for visualizing biological networks and systems thinking. The tool features interactive network visualization powered by Cytoscape.js, with real-time graph editing and manipulation capabilities. It supports JSON import/export and provides a responsive design that works seamlessly on the desktop (mobile-friendly version coming later). The tech stack combines modern frontend technologies with robust backend architecture. The frontend uses Next.js 14 with TypeScript and Cytoscape.js for the visualization engine. The backend is built with…
2025 · nodes.bio · its alternatives →
14
Speck, a WebGL molecule renderer▲20
Browser-based WebGL molecule renderer with the goal of producing figures that are as attractive as they are practical. - wwwtyro/speck
2016 · github.com · its alternatives →
15
Open-Source multi-dashboarding platform for teams and client reporting▲73
Open-source reporting platform to build and share live dashboards from APIs, SQL and NoSQL databases, with powerful AI assistant, scheduling, and embeddable charts 📈📊 - chartbrew/chartbrew
2021 · github.com · its alternatives →
16
Molecule – Streaming, zero-allocation protobuf decoding in Go▲70
Molecule is a Go library for parsing protobufs in an efficient and zero-allocation manner. - GitHub - richardartoul/molecule: Molecule is a Go library for parsing protobufs in an efficient and zero-allocation manner.
2020 · github.com · its alternatives →
17
SwimOS Rust – A framework for real-time streaming data applications▲71
2024 · github.com · its alternatives →
18
Modeling the human body in Rust so I can cmd+click through it▲46
I started this trying to understand two things: why my Asian friends turn red after drinking, and why several friends all seemed to have migraine clusters. I was reading medical papers and textbooks, but kept getting lost jumping between topics. I thought: what if I could just Cmd+Click through this like code? What if "ALDH2 gene" was actually clickable, and took me to the variant, the phenotype, the population frequencies? So I started modeling human biology in Rust with my Ralph agent (Claude in a loop, ty ghuntley). Turns out the type system is perfect for this. Every biological entity is…
2025 · github.com · its alternatives →
19
Embedded our open-source charting lib into a no-code storytelling tool▲13
Hi HN, We're a small team working on a new dataviz engine and its applications. We built our charting engine in C++ and run it on WebAssembly. Two years ago, we launched Vizzu as an open-source animated data visualization library aimed at JS developers, allowing users to create dynamic charts. We also released a Python wrapper under the name ipyvizzu for data scientists. Since then, we've been working hard to make this technology accessible to everyone, regardless of their coding skills. Today, we're proud to introduce our no-code storytelling tool. With this tool, anyone can turn their…
2024 · vizzu.io · its alternatives →
20SA
Spart – A Rust library for fast spatial search with Python bindings▲31
Hi everyone, I've made an open-source library for fast spatial search in Rust. It's called Spart, and it currently provides the following features: - Five tree implementations: Quadtree, Octree, Kd-tree, R-tree, and R*-tree - Python bindings (`pyspart` on PyPI) - Fast k-nearest neighbor (kNN) and radius search - Bulk data loading for efficient tree construction Project's GitHub repo: https://github.com/habedi/spart
2025 · its alternatives →
21
Minimalist library to generate SVG views of scientific data▲47
Just wanted to share with HN a simple/minimal open source Python library that generates SVG files visualizing two dimensional data and distributions, in case others find it useful or interesting. I wrote it as a fun project, mostly because I found that the standard libraries in Python generated unnecessarily large SVG files. One nice property is that I can configure the visuals through CSS, which allows me to support dark/light mode browser settings. The graphs are specified as JSON files (the repository includes a few examples). It supports scatterplots, line plots, histograms,…
Mar 2026 · github.com · its alternatives →
22T5
TensorBase: 5x~10000x Faster Drop-In/Accelerator for ClickHouse in Rust▲19
2021 · tensorbase.io · its alternatives →
23
Rust built open-sourced CLI tool for API specification validation▲23
Stop half-done APIs! Cherrybomb is a CLI tool that helps you avoid undefined user behaviour by auditing your API specifications, validating them and running API security tests. - blst-security/cherrybomb
2022 · github.com · its alternatives →
24
Open database of link metadata for large-scale analysis▲15
I would like to share an open database focused on link-level metadata extraction and aggregation, which may be of interest to researchers. The project maintains a structured dataset of links enriched with metadata such as: - page title - description / summary - publication date (when available) - thumbnail / preview image - etc. The goal is to provide a reusable, inspectable set of link metadata that can be used for experiments in areas such as: - RSS and feed analysis - news analysis - link rot analysis? The database is publicly available here:…
Jan 2026 · github.com · its alternatives →

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