BEER
Biophysical Evaluation Engine for Residues
All-in-one desktop tool for protein sequence analysis
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Every protein tells a story. BEER helps you read it.
From basic sequence properties to advanced disorder and aggregation predictions powered by ESM2 neural models and AlphaFold predictions, BEER delivers a full biophysical analysis of your protein in a single click — with interactive graphs, a 3D structure viewer, and publication-ready exports, all from one desktop application.
You don't need to jump between a dozen programs and servers to understand your protein any more. Relax and enjoy your BEER.
If you use BEER in your research, please cite: Mukherjee, S. arXiv:2504.20561 (2025). (https://doi.org/10.48550/arXiv.2504.20561)
What can BEER do?
Comprehensive Sequence Analysis
From physicochemical properties and charge patterning to disorder, aggregation, RNA binding, phase separation, and transmembrane topology — all computed locally, no internet required.
Interactive Graphs & 3D Structure
Explore publication-quality graphs across ten categories, and visualize your protein in 3D with multiple representations, colour modes, and one-click PNG export.
Built for Research Workflows
Fetch sequences directly from UniProt and RCSB, export full reports in CSV, JSON, PDF, or DAT, save and restore sessions, and compose custom multi-panel publication figures.
BEER can do much more!
BLAST: Submit any sequence to NCBI BLASTp and load any hit directly into BEER for immediate analysis.
Multichain Analysis: Analyze all chains from a multi-FASTA or multi-chain PDB simultaneously — compare mass, charge, and composition per chain.
Compare: Place two sequences side-by-side with a shared property table and overlaid disorder, hydrophobicity, and aggregation profiles.
Truncation Series: Sweep across progressive N- and C-terminal truncations and track how biophysical properties change along the sequence.
MSA Series: Paste a multi-sequence alignment and compute per-column conservation and residue covariance — useful for identifying functionally important positions.
Complex Mass: Define subunit stoichiometry and instantly compute the molecular weight and extinction coefficient of the full complex.
Getting started with BEER...
Step 1: Create environment and install BEER
conda create -n beer python=3.12 -y
conda activate beer
git clone https://github.com/chemgame/BEER.git
cd BEER
pip install .
Step 2: Install ESM2 neural prediction models
pip install "torch>=2.0" --index-url https://download.pytorch.org/whl/cpu
pip install fair-esm scipy
Step 3: Launch BEER
beer
Note: DeepTMHMM (transmembrane topology) is optional and requires pip install pybiolib. Linux users require additional Qt platform libraries — see the full installation guide on GitHub.
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