alterlab-esm

# ESM: Evolutionary Scale Modeling ## Overview ESM provides state-of-the-art protein language models for understanding, generating, and designing proteins. This skill enables working with two model families: ESM3 for generative protein design across sequence, structure, and function, and ESM C for efficient protein representation learning and embeddings. ## Core Capabilities ### 1. Protein Sequence Generation with ESM3 Generate novel protein sequences with desired properties using multimodal generative modeling. **When to use:** - Designing proteins with specific functional properties - Completing partial protein sequences - Generating variants of existing proteins - Creating proteins with desired structural characteristics **Basic usage:** ```python from esm.models.esm3 import ESM3 from esm.sdk.api import ESM3InferenceClient, ESMProtein, GenerationConfig # Load model locally model: ESM3InferenceClient = ESM3.from_pretrained("esm3-sm-open-v1").to("cuda") # Create protein prompt protein = ESMProtein(sequence="MPRT___KEND") # '_' represents masked positions # Generate completion protein = model.generate(protein, GenerationConfig(track="sequence", num_steps=8)) print(protein.sequence) ``` **For remote/cloud usage via Forge API:** ```python from esm.sdk.forge import ESM3ForgeInferenceClient from esm.sdk.api import ESMProtein, GenerationConfig # Connect to Forge model = ESM3ForgeInferenceClient(model="esm3-medium-2024-08", url="https://forge.evolutionaryscale.ai", t...