9 skills · sorted by relevance
Predict structures of protein, nucleic acid, and small-molecule complexes with ESMFold2, using single sequences or aligned related sequences. The skill also covers ESMC models for numerical sequence representations, mutation scoring, and predictions of contacts between residues.
Use Biohub’s Python SDK to complete protein sequences with ESM3, extract numerical sequence representations with ESMC, and predict all-atom structures with ESMFold2. The skill guides local or hosted inference, input validation, and output checks.
Protein language models through the EvolutionaryScale `esm` Python SDK. Generate and embed sequences with ESM3 (multimodal sequence, structure and function prompting), extract per-residue and mean-pooled embeddings with ESM C, fold sequences with ESMFold2, and run inference locally or against the Forge and Biohub hosted clients. Use this skill for protein representation learning, variant effect and mutational scanning from likelihoods, sequence generation and inpainting, structure prediction from sequence alone, and embedding features for downstream models. Also trigger on esm, ESM3, ESMC, ESM Cambrian, ESMFold2, `from esm.models`, ESMProtein, GenerationConfig, forge.evolutionaryscale.ai, biohub.ai, or ESM_API_KEY.
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Protein structure prediction from sequence. ESMFold-based, single GPU, no MSA needed. Predicts 3D structures with pLDDT confidence scores for drug discovery targets.
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Run protein structure prediction, molecular design, and docking tools on Tamarind Bio without a local GPU. Guides tool selection, input validation, job submission, batch processing, and result retrieval through its REST API or MCP server.
Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
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Use the fair-esm repository skill for protein language-model embeddings, ESMFold structure prediction, ESM-IF1 inverse folding, and zero-shot variant-effect scoring.
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Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.
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Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
The English summary is being prepared. Showing the original description.