Mol 1

Mol 1: Mol-1 is an open biomolecular intelligence tool that predicts 3D structures for proteins, DNA, RNA, ligands, and ions.

Mol-1 is an open biomolecular intelligence system that predicts structures for protein chains, DNA sequences, RNA sequences, ligands, and ions. It processes job descriptions provided as JSON, running inference to output CIF structures and confidence JSON files per sample. The tool supports features like MSA searches via MMseqs2 and HMMER, template alignments, and fine-tuning using custom mmCIF files. It includes a command-line interface with commands for inference, MSA search, preparation, structure conversion, and environment diagnostics. Designed for researchers and developers in computational biology, Mol-1 runs on CUDA-compatible GPUs and requires local setup with Python and specific driver dependencies.

Mol 1 at a glance

Best for: Researcher
Runs on: CLI, Python
Pricing: Free
Released: October 2026
Category: AI research tool
Website: github.com/molence/mol-1

Key features

Predicts biomolecular structures from JSON job descriptions
Performs protein and RNA multiple sequence alignment
Searches and aligns structural templates using HMMER
Supports model fine-tuning with custom mmCIF datasets
Converts PDB and CIF structures to Mol-1 JSON format
Performs environment diagnostics via built-in checks
Outputs CIF structures with confidence JSON per sample

Use it for

Predicting antibody-antigen complex structures
Running protein-ligand and molecular glue predictions
Analyzing protein-peptide complex benchmarks
Fine-tuning biomolecular models on custom training data

Alternatives to Mol 1

Biomni — Automates complex wet-lab experimental design with specialized tools and databases.
Open Science — Local-first design with persistent Python and R kernels and traceable artifacts.
Paper2Agent — It enables direct interaction with research papers and automatic result reproduction.
OpenClaw Medical Skills — Adds 869 clinical, genomic, and drug discovery skills to OpenClaw and NanoClaw agents.
Alphaprotein Novo — Co-generates protein structures and sequences for enzyme design.
OpenResearch — Run parallel research workflows locally or on remote compute.
DiscoveryRSI — Achieves high actionable-reference rates and supports multi-agent evolutionary research search.
Liatir App — Runs local analyses offline with managed AI models and scientific viewers.
Vegaml — Runs locally on your hardware with calibrated probabilities and conformal answer sets.
OpenMed — Runs 100 percent on-device without cloud calls or data sharing.
notebooklm-py — Automates research, content generation, and structured data export from notebooks.
Neuron Explorer — It keeps every rollout and maps model layers in perspective.

All Mol 1 alternatives